GSE217511
Chakkapong_Burudpakdee
2024-08-18
GSE217511- Single-nucleus transcriptomics atlas of middle and late prenatal human cortical development.
samples: Single-nucleus transcriptomics (snRNA-seq) data was generated from fresh-frozen, macrodissected germinal matrix and cortical plate of 15 prenatal, non-pathological human postmortem samples from second and third trimester gestation, and from fresh-frozen, macrodissected basal ganglia and neocortex of 3 adult, non-pathological human postmortem controls. The germinal matrix was macrodissected at the level of the caudothalamic groove and the cortical plate from the adjacent frontoparietal neocortex; grossly equal amount of subjacent white matter was included for both dissections. For prenatal tissues, to consistently dissect the posterior germinal zone in prenatal brains of varying size, the length of the entire cortical surface was measured for each sample and tissue from the ventricular to the apical surface was dissected in the area three fourths of the length from the rostral aspect. For adult tissues, the neocortex was dissected at the level of the pre-central gyrus, Brodmann area 4, and the subventricular zone plus caudate were dissected at the level of the posterior basal ganglia adjacent to the dissected neocortex.
Public on Dec 01, 2022
Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors.
Illumina NovaSeq 6000 (Homo sapiens)
Icahn School of Medicine at Mount Sinai
Susana R, Zarmeen M, Elisa F, Balagopal P, Bruno G, Robert S, Kristin B, Alexander T, Nadejda T
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## 17wks 20wks 22wks 26wks 28yrs 38wks 45yrs 53yrs
## 3000 3000 3000 3000 3000 3000 3000 3000## `geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'
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## Finding variable features for layer counts.17wks
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## Finding variable features for layer counts.45yrs
## Finding variable features for layer counts.53yrs## Warning in scale_x_log10(): log-10 transformation introduced infinite values.## Warning: Removed 2828 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Centering and scaling data matrix
## PC_ 1
## Positive: AGBL4, DLGAP2, FGF14, OPCML, FRMPD4, STXBP5L, RYR2, GRM5, CSMD1, CACNA2D3
## FGF12, MTUS2, RIMS2, KCNIP4, GRIN2A, CACNA1A, LINGO2, LRFN5, SYN3, KCNMA1
## KSR2, CNTNAP5, KCNQ5, RBFOX3, MIAT, SYN2, TENM2, PCSK2, ASIC2, ERC2
## Negative: QKI, ZBTB20, SLC1A3, FBXL7, COL4A5, NFIA, ADGRV1, ST18, MEIS2, SYNE2
## AL589740.1, NEAT1, DOCK5, CHD7, DAAM2, AC026316.5, ERBB4, DOCK1, CLMN, ENPP2
## TTYH2, ZFHX4, RFTN2, GLI3, SPP1, TF, FGFR2, LINC01965, RNF220, FA2H
## PC_ 2
## Positive: ROBO2, MAP1B, RBFOX1, SYT1, STMN2, SATB2, RALYL, KCNH7, TMSB10, PTPRD
## NELL2, DCLK1, EPHA5, UNC5D, KCNQ5, GRIN2B, CCBE1, FGF13, EPHA3, LINC01122
## ARPP21, SLC44A5, GRIA1, NKAIN2, KHDRBS2, PLXNA4, GRIP1, GAP43, KCNB2, SOX4
## Negative: CDH20, NEAT1, DOCK1, KANK1, FHIT, PDE4B, SLC1A3, DOCK5, SASH1, GRAMD2B
## GLUL, SPATA6, KAT2B, ATP1A2, ATP13A4, PREX2, SLC9A9, FBXL7, ATP10B, RFTN2
## MSI2, DOCK10, QKI, HIF3A, LMCD1-AS1, ZHX2, ZBTB20, FOXO1, HTRA1, GPC5
## PC_ 3
## Positive: MBP, ST18, AC026316.5, RNF220, TF, CLMN, ENPP2, CTNNA3, SYNJ2, HHIP
## CNP, CERCAM, SLC24A2, CDK18, SLC5A11, FA2H, DOCK5, DOCK10, UGT8, BCAS1
## EDIL3, PALM2, PLD1, AK5, SPOCK3, RAPGEF5, PDE1C, GPR37, CRYAB, PPM1H
## Negative: SLC1A2, PITPNC1, NKAIN3, RFX4, PTPRZ1, ADGRV1, ATP1A2, PARD3, PRDM16, GPC5
## ALDH1L1, HIF3A, RNF219-AS1, LINC00511, RGS20, BMPR1B, SLC4A4, CACHD1, MMD2, NHSL1
## SLC7A11, CTNNA2, SHROOM3, EYA2, F3, SPON1, RANBP3L, ARHGEF26, SOX6, PALLD
## PC_ 4
## Positive: AL117329.1, SPARCL1, CLU, ARHGAP26, CAMK2A, KIAA1211L, NRGN, CREG2, PHYHIP, NIPAL2
## CABP1, AC067956.1, CADPS2, AC011287.1, SLC22A10, CBLN2, CCK, LRRK1, ARHGAP24, LINC01250
## VSNL1, STAMBPL1, RFTN1, DOCK8, HTR2A, APBB1IP, FSTL4, CHN1, KCNH1, ADAM28
## Negative: PLPPR1, ANO4, KIAA1211, MYO16, FGF13, XKR4, PTPRD, SEMA6D, SCN9A, LUZP2
## ROBO1, SLC44A5, SLC24A3, TENM1, DAB1, CCBE1, KLHL1, HIP1, FRMD3, KCNH8
## ROBO2, KCNQ1OT1, GRIP1, ST8SIA2, C8orf34, RUNX1T1, FRMD4B, TMEM108, PROM1, AFF2
## PC_ 5
## Positive: DOCK8, APBB1IP, ADAM28, SLCO2B1, TBXAS1, INPP5D, RHBDF2, C3, FYB1, CSF2RA
## LRMDA, DOCK2, PALD1, SP100, RCSD1, FLI1, AC074327.1, ARHGAP15, AOAH, ST6GAL1
## ATP8B4, MYO1F, ARHGAP25, RUNX1, LPCAT2, RBM47, PIK3AP1, A2M, DENND3, RASGEF1C
## Negative: CLU, SPARCL1, NPAS3, AL117329.1, NRXN3, DGKB, TMEM132D, ERBB4, GPC5, CREG2
## CAMK2A, KCTD8, KCND3, CABP1, PHYHIP, KCNH1, PDE7B, CCK, NCAM2, RHBDL3
## RORA, PAM, COBL, AC067956.1, ZMAT4, ADGRV1, SLC22A10, CBLN2, AQP4-AS1, RFX4
## used (Mb) gc trigger (Mb) max used (Mb)
## Ncells 10512971 561.5 25286841 1350.5 25286841 1350.5
## Vcells 1259276257 9607.6 2390062654 18234.8 2390055696 18234.7## Computing nearest neighbor graph
## Computing SNN## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
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## Number of nodes: 23124
## Number of edges: 788500
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## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.9855
## Number of communities: 10
## Elapsed time: 1 seconds## Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
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## This message will be shown once per session## 22:10:58 UMAP embedding parameters a = 0.9922 b = 1.112
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## 22:11:06 Annoy recall = 100%
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## 22:11:07 Initializing from normalized Laplacian + noise (using RSpectra)
## 22:11:08 Commencing optimization for 200 epochs, with 982644 positive edges
## 22:11:15 Optimization finished
## [1] "excitatory_neurons2" "inhibitory_neurons" "early_neurons"
## [4] "excitatory_neurons1" "opc" "oligodendrocytes"
## [7] "bipolar_neurons" "mature_neurons" "microglia"
## [10] "astrocytes"
##
## excitatory_neurons2 inhibitory_neurons early_neurons excitatory_neurons1
## 5507 3732 3374 2290
## opc oligodendrocytes bipolar_neurons mature_neurons
## 1895 1767 1603 1394
## microglia astrocytes
## 973 589## orig.ident nCount_RNA nFeature_RNA percent.mt
## AAACCCAGTGCTTATG-1_1 17wks 4588 2013 0.1743679
## AAACGAAAGCCTCTTC-1_1 17wks 513 420 1.9493177
## AAACGAACAACAAAGT-1_1 17wks 457 375 0.4376368
## AAACGAACAACACGTT-1_1 17wks 452 381 0.4424779
## AAACGAATCCAATCTT-1_1 17wks 484 392 2.4793388
## AAACGCTAGAGGATGA-1_1 17wks 479 378 0.4175365
## RNA_snn_res.0.05 seurat_clusters cell_types
## AAACCCAGTGCTTATG-1_1 1 1 inhibitory_neurons
## AAACGAAAGCCTCTTC-1_1 1 1 inhibitory_neurons
## AAACGAACAACAAAGT-1_1 1 1 inhibitory_neurons
## AAACGAACAACACGTT-1_1 1 1 inhibitory_neurons
## AAACGAATCCAATCTT-1_1 1 1 inhibitory_neurons
## AAACGCTAGAGGATGA-1_1 1 1 inhibitory_neurons##
## 17wks 20wks 22wks 26wks 38wks 28yrs 45yrs 53yrs
## 2996 2912 2994 2954 2945 2803 2701 2819## Warning: Monocle 3 trajectories require cluster partitions, which Seurat does
## not calculate. Please run 'cluster_cells' on your cell_data_set object## DataFrame with 6 rows and 9 columns
## orig.ident nCount_RNA nFeature_RNA percent.mt
## <character> <numeric> <integer> <numeric>
## AAACCCAGTGCTTATG-1_1 17wks 4588 2013 0.174368
## AAACGAAAGCCTCTTC-1_1 17wks 513 420 1.949318
## AAACGAACAACAAAGT-1_1 17wks 457 375 0.437637
## AAACGAACAACACGTT-1_1 17wks 452 381 0.442478
## AAACGAATCCAATCTT-1_1 17wks 484 392 2.479339
## AAACGCTAGAGGATGA-1_1 17wks 479 378 0.417537
## RNA_snn_res.0.05 seurat_clusters cell_types
## <factor> <factor> <factor>
## AAACCCAGTGCTTATG-1_1 1 1 inhibitory_neurons
## AAACGAAAGCCTCTTC-1_1 1 1 inhibitory_neurons
## AAACGAACAACAAAGT-1_1 1 1 inhibitory_neurons
## AAACGAACAACACGTT-1_1 1 1 inhibitory_neurons
## AAACGAATCCAATCTT-1_1 1 1 inhibitory_neurons
## AAACGCTAGAGGATGA-1_1 1 1 inhibitory_neurons
## ident Size_Factor
## <factor> <numeric>
## AAACCCAGTGCTTATG-1_1 17wks 4588
## AAACGAAAGCCTCTTC-1_1 17wks 513
## AAACGAACAACAAAGT-1_1 17wks 457
## AAACGAACAACACGTT-1_1 17wks 452
## AAACGAATCCAATCTT-1_1 17wks 484
## AAACGCTAGAGGATGA-1_1 17wks 479## | | | 0% | |======================================================================| 100%## Cells aren't colored in a way that allows them to be grouped.
## No preprocess_method specified, using preprocess_method = 'PCA'## | | | 0% | |======================================================================| 100%
## | | | 0% | |======================================================================| 100%
## | | | 0% | |======================================================================| 100%
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## | | | 0% | |======================================================================| 100%
## | | | 0% | |======================================================================| 100%
## | | | 0% | |======================================================================| 100%
## | | | 0% | |======================================================================| 100%
## | | | 0% | |======================================================================| 100%## orig.ident nCount_RNA nFeature_RNA percent.mt
## AAACCCAGTGCTTATG-1_1 17wks 4588 2013 0.1743679
## AAACGAAAGCCTCTTC-1_1 17wks 513 420 1.9493177
## AAACGAACAACAAAGT-1_1 17wks 457 375 0.4376368
## AAACGAACAACACGTT-1_1 17wks 452 381 0.4424779
## AAACGAATCCAATCTT-1_1 17wks 484 392 2.4793388
## AAACGCTAGAGGATGA-1_1 17wks 479 378 0.4175365
## RNA_snn_res.0.05 seurat_clusters cell_types
## AAACCCAGTGCTTATG-1_1 1 1 inhibitory_neurons
## AAACGAAAGCCTCTTC-1_1 1 1 inhibitory_neurons
## AAACGAACAACAAAGT-1_1 1 1 inhibitory_neurons
## AAACGAACAACACGTT-1_1 1 1 inhibitory_neurons
## AAACGAATCCAATCTT-1_1 1 1 inhibitory_neurons
## AAACGCTAGAGGATGA-1_1 1 1 inhibitory_neurons
## monocle_pseudotime
## AAACCCAGTGCTTATG-1_1 5.600102e-02
## AAACGAAAGCCTCTTC-1_1 4.491611e-01
## AAACGAACAACAAAGT-1_1 1.174419e-01
## AAACGAACAACACGTT-1_1 1.326792e-06
## AAACGAATCCAATCTT-1_1 5.659887e-01
## AAACGCTAGAGGATGA-1_1 4.665123e-01## 22:13:23 UMAP embedding parameters a = 0.9922 b = 1.112
## 22:13:23 Read 23124 rows and found 15 numeric columns
## 22:13:23 Using Annoy for neighbor search, n_neighbors = 30
## 22:13:23 Building Annoy index with metric = cosine, n_trees = 50
## 0% 10 20 30 40 50 60 70 80 90 100%
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## 22:13:24 Writing NN index file to temp file /tmp/RtmpXcOcdQ/file55e93c9cd067
## 22:13:24 Searching Annoy index using 1 thread, search_k = 3000
## 22:13:30 Annoy recall = 100%
## 22:13:31 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
## 22:13:32 Initializing from normalized Laplacian + noise (using RSpectra)
## 22:13:33 Commencing optimization for 200 epochs, with 982644 positive edges
## 22:13:41 Optimization finished## Warning: Number of dimensions changing from 2 to 3## orig.ident nCount_RNA nFeature_RNA percent.mt
## AAACCCAGTGCTTATG-1_1 17wks 4588 2013 0.1743679
## AAACGAAAGCCTCTTC-1_1 17wks 513 420 1.9493177
## AAACGAACAACAAAGT-1_1 17wks 457 375 0.4376368
## AAACGAACAACACGTT-1_1 17wks 452 381 0.4424779
## AAACGAATCCAATCTT-1_1 17wks 484 392 2.4793388
## AAACGCTAGAGGATGA-1_1 17wks 479 378 0.4175365
## RNA_snn_res.0.05 seurat_clusters cell_types
## AAACCCAGTGCTTATG-1_1 1 1 inhibitory_neurons
## AAACGAAAGCCTCTTC-1_1 1 1 inhibitory_neurons
## AAACGAACAACAAAGT-1_1 1 1 inhibitory_neurons
## AAACGAACAACACGTT-1_1 1 1 inhibitory_neurons
## AAACGAATCCAATCTT-1_1 1 1 inhibitory_neurons
## AAACGCTAGAGGATGA-1_1 1 1 inhibitory_neurons
## monocle_pseudotime
## AAACCCAGTGCTTATG-1_1 5.600102e-02
## AAACGAAAGCCTCTTC-1_1 4.491611e-01
## AAACGAACAACAAAGT-1_1 1.174419e-01
## AAACGAACAACACGTT-1_1 1.326792e-06
## AAACGAATCCAATCTT-1_1 5.659887e-01
## AAACGCTAGAGGATGA-1_1 4.665123e-01Neural network predictive classifications by paired neuro-developmental time-points in order.
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## dotplot##
## Attaching package: 'caret'## The following objects are masked from 'package:InformationValue':
##
## confusionMatrix, precision, sensitivity, specificity## The following object is masked from 'package:monocle3':
##
## compare_models## The following object is masked from 'package:purrr':
##
## lift##
## 17wks 20wks 22wks 26wks 28yrs 38wks 45yrs 53yrs
## 2996 2912 2994 2954 2803 2945 2701 2819##
## excitatory_neurons2 inhibitory_neurons early_neurons excitatory_neurons1
## 5507 3732 3374 2290
## opc oligodendrocytes bipolar_neurons mature_neurons
## 1895 1767 1603 1394
## microglia astrocytes
## 973 589
## Prediction/classification_results:## 0 1
## 1531 1392## Actual_classifications:##
## 0 1
## 1451 1472## Confusion Matrix and Statistics
##
## Reference
## Prediction 0 1
## 0 1328 203
## 1 123 1269
##
## Accuracy : 0.8885
## 95% CI : (0.8765, 0.8997)
## No Information Rate : 0.5036
## P-Value [Acc > NIR] : < 2.2e-16
##
## Kappa : 0.777
##
## Mcnemar's Test P-Value : 1.212e-05
##
## Sensitivity : 0.8621
## Specificity : 0.9152
## Pos Pred Value : 0.9116
## Neg Pred Value : 0.8674
## Prevalence : 0.5036
## Detection Rate : 0.4341
## Detection Prevalence : 0.4762
## Balanced Accuracy : 0.8887
##
## 'Positive' Class : 1
## ## Setting levels: control = 0, case = 1## Warning in roc.default(response, predictor, auc = TRUE, ...): Deprecated use a
## matrix as predictor. Unexpected results may be produced, please pass a numeric
## vector.## Setting direction: controls < cases## Area under the curve: 0.9099## Length Class Mode
## call 6 -none- call
## response 2985 -none- numeric
## covariate 62685 -none- numeric
## model.list 2 -none- list
## err.fct 1 -none- function
## act.fct 1 -none- function
## linear.output 1 -none- logical
## data 21836 data.frame list
## exclude 0 -none- NULL
## net.result 1 -none- list
## weights 1 -none- list
## generalized.weights 1 -none- list
## startweights 1 -none- list
## result.matrix 708 -none- numeric
## Setting levels: control = 0, case = 1## Warning in roc.default(x, predictor, plot = TRUE, ...): Deprecated use a matrix
## as predictor. Unexpected results may be produced, please pass a numeric vector.## Setting direction: controls < cases
## PC_ 1
## Positive: AL589740.1, ADGRV1, LINC01965, MEIS2, SYNE2, GLI3, NKAIN3, NFIA, CENPF, DACH1
## SFRP1, FABP7, DIAPH3, VIM, HMGCS1, AC131571.1, UNC5D, SOX6, SMC4, LTBP1
## SOX4, ZFHX4, HMGB2, PDGFD, EPHA3, ZBTB20, IQGAP2, AC016205.1, GPC6, ASPM
## Negative: CSMD1, OPCML, NTRK2, KCNMA1, FGF14, FGF12, LRP1B, XKR4, DPP10, FRMPD4
## CACNA1A, CNTN1, SYN3, GRIN2B, KAZN, MAGI2, RYR2, PDZD2, RIMS2, GAS7
## CNTNAP5, LRRC4C, CELF4, GRM5, KHDRBS3, CACNA2D3, TENM2, SPOCK1, LINGO2, GABRG3
## PC_ 2
## Positive: GRIK3, HS3ST4, TP53I11, TMSB10, TRPM3, SORCS1, SCUBE1, CRYM, GAS7, SYT6
## PCP4, KIAA1217, STMN2, COL12A1, CALN1, NGEF, ISLR2, OSBPL10, IGSF21, GSG1L
## PAPPA2, TLE4, SLIT1, LMO3, GNAL, PDZD2, TRMT9B, FAM160A1, COL15A1, CELF4
## Negative: RORA, NPAS3, ZBTB20, MSI2, LSAMP, QKI, PRDM16, SLC1A3, FBXL7, EEPD1
## PTPRK, LRIG1, ZEB1, DTNA, SEZ6L, TNC, MAST4, LTBP1, NCAM2, GLI2
## CREB5, GLI3, GRIA4, TMTC2, ARAP2, AC092691.1, CDH20, FHIT, DOCK1, PTPRM
## PC_ 3
## Positive: NFIA, GLI3, SEL1L3, IGF2BP2, TLE4, PRDM16, CELSR1, PAX6, TP53I11, GRIK3
## PTN, SCUBE1, BOC, LINC01965, SYNE2, PLCE1, VCAN, ADGRV1, SEMA5B, NNAT
## GLI2, SHROOM3, LTBP1, CA12, IQGAP2, NKAIN3, LAMA1, HS3ST4, TMEM132B, ISLR2
## Negative: NRXN3, DLGAP2, THRB, GRM7, KCNIP4, UNC5C, ERBB4, IQCJ-SCHIP1, GRIA4, FMN1
## ZNF804B, NRGN, EDIL3, RASGRF2, CNTNAP2, ADARB2, MYRIP, CADPS2, PDZRN3, FAM19A1
## NWD2, ZBTB16, NECAB1, MBP, ANO3, PPFIBP1, NKAIN2, NEFL, SPARCL1, KCNC2
## PC_ 4
## Positive: LINC00854, BCAN, MMD2, KAZN, TCF7L1, COL20A1, HES4, TNC, LAMA4, EGFR
## HBA2, MECOM, EPN2, WSCD1, PLEKHH2, ARHGAP31, RHOJ, SEZ6L, XYLT1, MFGE8
## RPS23, HES5, FGFR1, RGMA, HES1, GRIK3, HIP1, MAML2, MAMDC2, ATP13A4
## Negative: AL589740.1, UNC5D, ROBO2, EPHA3, NKAIN3, EPHA5, KCNH7, MEIS2, NKAIN2, MAP1B
## PTPRD, ADGRV1, LINC01965, ROBO1, ELAVL2, SYT1, NFIA, SORBS2, ERBB4, MARCH1
## GPC6, HMGCS1, SEMA3C, CNR1, PDE4D, CNTNAP2, GRAMD1B, SNTG1, ZBTB20, SYNE2
## PC_ 5
## Positive: TNC, EEPD1, ID4, SFRP1, LRRC3B, SLCO1C1, MOXD1, AC131571.1, IQGAP2, VIM
## FABP7, FAM107A, HMGCS1, PTN, CCDC175, LAMA1, VEPH1, HES5, MAST4, FSTL1
## PARD3B, TMEM132B, PTPRM, RHOJ, GLI3, DOK5, SLC2A3, MMD2, SHROOM3, MFGE8
## Negative: NUSAP1, C21orf58, KNL1, KIF11, CDC25C, ASPM, TPX2, KIF15, KIF14, SPC25
## APOLD1, NUF2, POLQ, DIAPH3, CENPE, TACC3, CENPF, BRIP1, HMGB2, SMC4
## PARPBP, SGO2, WDR62, MIS18BP1, ECT2, FANCI, STIL, LINC01572, RTKN2, CEP152## 22:15:42 UMAP embedding parameters a = 0.9922 b = 1.112## 22:15:42 Read 5908 rows and found 15 numeric columns## 22:15:42 Using Annoy for neighbor search, n_neighbors = 30## 22:15:42 Building Annoy index with metric = cosine, n_trees = 50## 0% 10 20 30 40 50 60 70 80 90 100%## [----|----|----|----|----|----|----|----|----|----|## **************************************************|
## 22:15:42 Writing NN index file to temp file /tmp/RtmpXcOcdQ/file55e96d3d7cb7
## 22:15:42 Searching Annoy index using 1 thread, search_k = 3000
## 22:15:44 Annoy recall = 100%
## 22:15:45 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
## 22:15:46 Initializing from normalized Laplacian + noise (using RSpectra)
## 22:15:46 Commencing optimization for 500 epochs, with 244952 positive edges
## 22:15:51 Optimization finished## orig.ident nCount_RNA nFeature_RNA percent.mt
## AAACCCAGTGCTTATG-1_1 17wks 4588 2013 0.1743679
## AAACGAAAGCCTCTTC-1_1 17wks 513 420 1.9493177
## AAACGAACAACAAAGT-1_1 17wks 457 375 0.4376368
## AAACGAACAACACGTT-1_1 17wks 452 381 0.4424779
## AAACGAATCCAATCTT-1_1 17wks 484 392 2.4793388
## AAACGCTAGAGGATGA-1_1 17wks 479 378 0.4175365
## RNA_snn_res.0.05 seurat_clusters cell_types
## AAACCCAGTGCTTATG-1_1 1 1 inhibitory_neurons
## AAACGAAAGCCTCTTC-1_1 1 1 inhibitory_neurons
## AAACGAACAACAAAGT-1_1 1 1 inhibitory_neurons
## AAACGAACAACACGTT-1_1 1 1 inhibitory_neurons
## AAACGAATCCAATCTT-1_1 1 1 inhibitory_neurons
## AAACGCTAGAGGATGA-1_1 1 1 inhibitory_neurons##
## excitatory_neurons2 inhibitory_neurons early_neurons excitatory_neurons1
## 5507 3732 3374 2290
## opc oligodendrocytes bipolar_neurons mature_neurons
## 1895 1767 1603 1394
## microglia astrocytes
## 973 589##
## 20wks 22wks
## 2912 2994##
## 0 1
## 2912 2994##
## 0 1
## 2912 2994##
## 0 1
## 1506 1478##
## 0 1
## 1406 1516
## Prediction/classification_results:## 0 1
## 1466 1456## Actual_classifications:##
## 0 1
## 1406 1516## Confusion Matrix and Statistics
##
## Reference
## Prediction 0 1
## 0 1205 261
## 1 201 1255
##
## Accuracy : 0.8419
## 95% CI : (0.8281, 0.8549)
## No Information Rate : 0.5188
## P-Value [Acc > NIR] : < 2.2e-16
##
## Kappa : 0.6838
##
## Mcnemar's Test P-Value : 0.006052
##
## Sensitivity : 0.8278
## Specificity : 0.8570
## Pos Pred Value : 0.8620
## Neg Pred Value : 0.8220
## Prevalence : 0.5188
## Detection Rate : 0.4295
## Detection Prevalence : 0.4983
## Balanced Accuracy : 0.8424
##
## 'Positive' Class : 1
## ## Setting levels: control = 0, case = 1## Warning in roc.default(response, predictor, auc = TRUE, ...): Deprecated use a
## matrix as predictor. Unexpected results may be produced, please pass a numeric
## vector.## Setting direction: controls < cases## Area under the curve: 0.9047## Length Class Mode
## call 6 -none- call
## response 2984 -none- numeric
## covariate 41776 -none- numeric
## model.list 2 -none- list
## err.fct 1 -none- function
## act.fct 1 -none- function
## linear.output 1 -none- logical
## data 21836 data.frame list
## exclude 0 -none- NULL
## net.result 1 -none- list
## weights 1 -none- list
## generalized.weights 1 -none- list
## startweights 1 -none- list
## result.matrix 568 -none- numeric
## Setting levels: control = 0, case = 1## Warning in roc.default(x, predictor, plot = TRUE, ...): Deprecated use a matrix
## as predictor. Unexpected results may be produced, please pass a numeric vector.## Setting direction: controls < cases
## PC_ 1
## Positive: MAP1B, HBA2, ERBB4, PCDH11Y, NEFM, FABP7, ROBO2, HBA1, DLX6-AS1, SATB2
## PTPRD, MECOM, NUSAP1, ZNF804B, TMSB10, MAMDC2, FAM19A1, PRSS12, TNC, KNL1
## STMN2, RPS23, HES5, COL20A1, NPAS1, SEMA5B, ASPM, NKAIN2, AC016708.1, PTPRZ1
## Negative: KCNMA1, NTRK2, CACNA1A, CELF4, SYN3, GRID1, DANT2, CACNA2D3, ASTN2, SLC24A2
## AGBL4, SAMD12, NRCAM, NTRK3, ASIC2, CACNA1D, SYN2, TMEM132B, SPOCK1, SGSM1
## SLCO3A1, MTUS2, GABRG3, FGF14, MCF2L2, CACNA1E, SNAP25, CNTNAP5, ADCY2, KAZN
## PC_ 2
## Positive: SLC1A3, ZBTB20, MSI2, RORA, QKI, PRDM16, NPAS3, TNC, FBXL7, ADGRV1
## GLI3, EEPD1, ZEB1, TMTC2, EGFR, LTBP1, LRIG1, SEZ6L, AL589740.1, GLI2
## DOCK1, CREB5, TCF7L1, LINC01965, TMEM132D, PARD3B, COL11A1, BCAN, PAX6, LAMA1
## Negative: HS3ST4, GRIK3, TRPM3, SORCS1, TP53I11, SCUBE1, RBFOX1, CRYM, CALN1, ROBO2
## KIAA1217, IGSF21, ARPP21, OSBPL10, SYT6, PTPRD, XKR4, PCP4, COL12A1, PAPPA2
## STMN2, DPP10, TLE4, C8orf34, ISLR2, LMO3, NGEF, GNAL, SATB2, TMSB10
## PC_ 3
## Positive: GRIK3, RPS23, TMSB10, SEL1L3, LINC00854, TP53I11, MECOM, HS3ST4, PTPRZ1, SCUBE1
## TLE4, SEMA5B, MAMDC2, SORCS1, TNC, PRDM16, HES4, KAZN, CRYM, PCP4
## NNAT, SYT6, PITPNC1, PLEKHH2, GLI2, C21orf58, MMD2, XYLT1, PLCE1, GSG1L
## Negative: NKAIN2, NRXN3, PTPRD, GRM7, ERBB4, PTPRK, CNTNAP2, FAM19A1, ZNF804B, KCNIP4
## IQCJ-SCHIP1, MACROD2, ADGRL3, KCNQ5, RUNX1T1, CTNNA2, SYT1, RALYL, UNC5D, MAGI2
## SLC44A5, LSAMP, PDE4D, UNC5C, MAP1B, GRIK2, KCNH7, CSMD3, SNTG1, MARCH1
## PC_ 4
## Positive: HBA2, HBA1, TMSB10, FTL, FTH1, DSCAML1, ADARB2, MAMDC2, CELF4, FN1
## MECOM, PCSK1N, FLI1, CACNA1A, IGFBP7, CACNA2D3, NPAS1, NGEF, XAF1, RIPOR2
## ASIC2, SLIT3, SPARC, SAT1, SLC7A5, MIR4435-2HG, A2M, ZBTB16, AC092683.1, EBF1
## Negative: ROBO2, PTPRD, PCDH11Y, SATB2, KCNH7, SLC44A5, NKAIN2, MAP1B, RALYL, PTPRK
## LRRC4C, DOK5, CELF2, NELL2, PTPRZ1, MGAT4C, ZNF804B, FAM19A1, ARPP21, KCNQ5
## SEMA6D, LSAMP, AL589740.1, MACROD2, KLHL1, C21orf58, FAM155A, PRDM16, NRG3, UNC5D
## PC_ 5
## Positive: TNC, EEPD1, MMD2, PTPRZ1, GFAP, BCAN, LRP1B, RHOJ, MFGE8, SLC1A3
## ATP1A2, TCF7L1, SLCO1C1, RGMA, RGS20, HES5, LRIG1, ACSBG1, DTNA, RGS6
## PON2, ATP13A4, LRRC4C, FAM107A, PLEKHH2, COL27A1, ITPR2, LRRTM4, RFX4, HOPX
## Negative: NUSAP1, C21orf58, KNL1, ASPM, APOLD1, NPAS1, SOX4, KIF11, NUF2, KIF15
## KIF14, TPX2, ST8SIA2, HMGB2, POLQ, HBA2, CENPE, CENPF, TMSB10, SMC4
## TACC3, LHX6, LINC00854, GAD2, BRIP1, DIAPH3, DLX6-AS1, NNAT, AC016708.1, ECT2
## 22:19:21 UMAP embedding parameters a = 0.9922 b = 1.112
## 22:19:21 Read 5906 rows and found 15 numeric columns
## 22:19:21 Using Annoy for neighbor search, n_neighbors = 30
## 22:19:21 Building Annoy index with metric = cosine, n_trees = 50
## 0% 10 20 30 40 50 60 70 80 90 100%
## [----|----|----|----|----|----|----|----|----|----|
## **************************************************|
## 22:19:22 Writing NN index file to temp file /tmp/RtmpXcOcdQ/file55e9213cdd31
## 22:19:22 Searching Annoy index using 1 thread, search_k = 3000
## 22:19:23 Annoy recall = 100%
## 22:19:24 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
## 22:19:25 Initializing from normalized Laplacian + noise (using RSpectra)
## 22:19:25 Commencing optimization for 500 epochs, with 250192 positive edges
## 22:19:31 Optimization finished##
## excitatory_neurons2 inhibitory_neurons early_neurons excitatory_neurons1
## 5507 3732 3374 2290
## opc oligodendrocytes bipolar_neurons mature_neurons
## 1895 1767 1603 1394
## microglia astrocytes
## 973 589##
## 22wks 26wks
## 2994 2954## orig.ident nCount_RNA nFeature_RNA percent.mt
## AAACCCAGTTCACGAT-1_3 22wks 333 290 0.0000000
## AAACGAAAGGGACACT-1_3 22wks 371 298 0.0000000
## AAACGAACACAGTCCG-1_3 22wks 358 301 1.3966480
## AAACGAACATTACGGT-1_3 22wks 340 287 0.0000000
## AAACGAAGTAGACAGC-1_3 22wks 325 294 0.6153846
## AAACGCTAGCCTAGGA-1_3 22wks 360 298 0.0000000
## RNA_snn_res.0.05 seurat_clusters cell_types
## AAACCCAGTTCACGAT-1_3 0 0 excitatory_neurons2
## AAACGAAAGGGACACT-1_3 0 0 excitatory_neurons2
## AAACGAACACAGTCCG-1_3 0 0 excitatory_neurons2
## AAACGAACATTACGGT-1_3 0 0 excitatory_neurons2
## AAACGAAGTAGACAGC-1_3 0 0 excitatory_neurons2
## AAACGCTAGCCTAGGA-1_3 0 0 excitatory_neurons2
## Prediction/classification_results:## 0 1
## 1515 1428## Actual_classifications:##
## 0 1
## 1450 1493## Confusion Matrix and Statistics
##
## Reference
## Prediction 0 1
## 0 1353 162
## 1 97 1331
##
## Accuracy : 0.912
## 95% CI : (0.9012, 0.922)
## No Information Rate : 0.5073
## P-Value [Acc > NIR] : < 2.2e-16
##
## Kappa : 0.8241
##
## Mcnemar's Test P-Value : 6.986e-05
##
## Sensitivity : 0.8915
## Specificity : 0.9331
## Pos Pred Value : 0.9321
## Neg Pred Value : 0.8931
## Prevalence : 0.5073
## Detection Rate : 0.4523
## Detection Prevalence : 0.4852
## Balanced Accuracy : 0.9123
##
## 'Positive' Class : 1
## ## Setting levels: control = 0, case = 1## Warning in roc.default(response, predictor, auc = TRUE, ...): Deprecated use a
## matrix as predictor. Unexpected results may be produced, please pass a numeric
## vector.## Setting direction: controls < cases## Area under the curve: 0.9456## Length Class Mode
## call 6 -none- call
## response 3005 -none- numeric
## covariate 60100 -none- numeric
## model.list 2 -none- list
## err.fct 1 -none- function
## act.fct 1 -none- function
## linear.output 1 -none- logical
## data 21836 data.frame list
## exclude 0 -none- NULL
## net.result 1 -none- list
## weights 1 -none- list
## generalized.weights 1 -none- list
## startweights 1 -none- list
## result.matrix 688 -none- numeric
## Setting levels: control = 0, case = 1## Warning in roc.default(x, predictor, plot = TRUE, ...): Deprecated use a matrix
## as predictor. Unexpected results may be produced, please pass a numeric vector.## Setting direction: controls < cases
## PC_ 1
## Positive: ERBB4, ZEB1, MAP1B, NPAS3, SOX6, TMSB10, SLC1A3, SPARCL1, FTH1, CLU
## SYNE2, QKI, CHD7, ZBTB20, GAPDH, GLI3, AL589740.1, NEFM, NEAT1, COL4A5
## RPS23, FTL, NEFL, SPP1, ZFP36L1, DOCK5, ITPR2, ZFHX4, LINC00609, BCAS1
## Negative: CHRM2, PCSK2, HTR7, TENM1, AC060809.1, CCBE1, SCN9A, CACNA1E, MYO16, CALN1
## RYR3, DYNC1I1, GRM1, FGF13, PTCHD1-AS, PROM1, MIR137HG, SYN3, PRR16, XKR4
## SEMA6D, PLPPR1, ANKRD30BL, KCNJ6, C8orf34, FRMD3, GRIA1, SPHKAP, PPFIBP1, HS3ST2
## PC_ 2
## Positive: KCNIP1, NPAS3, MSI2, KAT2B, FBXL7, MAGI1, GPC5, QKI, ARHGAP42, LINC00854
## PARD3, SLC1A3, LRIG1, TCF7L2, ZEB1, SPATA6, PRKD1, SLC1A2, CDH20, DOCK1
## ATP13A4, CHD7, TNS1, MMD2, LINC00511, CECR2, RFTN2, DPF3, EPN2, SEMA5A
## Negative: SATB2, NKAIN2, PTPRD, RALYL, ROBO2, ARPP21, MAP1B, ZNF804B, FAM19A1, CCBE1
## KLHL1, KCNQ5, RBFOX1, MIR137HG, SLC44A5, NELL2, MGAT4C, KHDRBS2, IQCJ-SCHIP1, PTPRK
## C8orf34, PCDH11Y, SCN9A, KCNH7, SAMD3, ADAMTSL3, MACROD2, CELF2, HTR7, GRM7
## PC_ 3
## Positive: FOXP1, KCNMA1, POU6F2, MAP3K5, PTPRK, RAPGEF5, ARAP2, RYR2, LDB2, ZFPM2
## ANO3, PRKCB, UNC5C, PTCHD1-AS, NECAB1, CSGALNACT1, TMEM132D, IQCJ-SCHIP1, TMEM132B, CDH20
## NPNT, SPARCL1, CALN1, PLXDC2, KCNIP4, RALYL, PEX5L, EFNA5, AC006148.1, NPAS2
## Negative: DLX6-AS1, ERBB4, LINC00854, ARHGAP28, GAD1, ADARB2, DSCAML1, NPAS1, IGF1, MAF
## PDZRN3, NXPH1, RIPOR2, NXPH2, PLS3, GAD2, KIAA1211, DLX1, RUNX1T1, ELFN1
## NETO2, HUNK, GAS2L3, KITLG, GRIP2, NTN4, THRB, GRIA1, NYAP2, MCUB
## PC_ 4
## Positive: FAM19A1, PRSS12, SPON1, PID1, AL589740.1, DCC, LINC00854, SLC44A5, CCBE1, MDGA1
## SEZ6L, CDH4, UNC5D, CUX2, NHSL1, PTPRK, CECR2, AC007402.1, NPNT, KCNH7
## ZBTB20, CDH13, EPHA3, ZNF804A, TOX3, AC092691.1, SATB2, LSAMP, UACA, LDLRAD4
## Negative: KIAA1217, OLFM3, TRPM3, HS3ST4, GRIK3, CDH18, SLC35F3, GALNT17, GABRG3, CACNA2D3
## CELF4, TSHZ3, ASIC2, SORCS1, DLC1, SPOCK3, FAM160A1, SNRPN, AC025809.1, ZNF385D
## SAMD12, SYNPR, MLIP, ABLIM3, CDH9, PEX5L, VSNL1, LINC02223, GRIN3A, HSPA12A
## PC_ 5
## Positive: FAM19A2, ANO3, GRIA4, KCNC2, GALNTL6, RASGRF2, FMN1, KCNIP4, CUX2, MYRIP
## THSD4, PDZRN3, IQCJ-SCHIP1, KCNH5, NECTIN3, CYP1B1-AS1, PTCHD1-AS, EPHA6, SYNDIG1, RARB
## RCAN2, NWD2, ITPR1, PPFIBP1, AJ009632.2, TMTC1, PLCH1, RSPO2, PTCHD4, KCTD16
## Negative: FAM160A1, EPB41L4A, HS3ST4, TLE4, COL15A1, BRINP3, LINC02223, HCRTR2, DLC1, TRPM3
## KLHL1, PRKG1, AC004158.1, COL12A1, LMO3, GRIK3, LINC01776, AL133346.1, DSCAM, ROBO2
## ZFHX3, TRMT9B, SEMA3C, CDH11, AP001636.3, FOXP2, DCC, NFIA, AC007656.1, FSTL5
## 22:21:01 UMAP embedding parameters a = 0.9922 b = 1.112
## 22:21:01 Read 5948 rows and found 15 numeric columns
## 22:21:01 Using Annoy for neighbor search, n_neighbors = 30
## 22:21:01 Building Annoy index with metric = cosine, n_trees = 50
## 0% 10 20 30 40 50 60 70 80 90 100%
## [----|----|----|----|----|----|----|----|----|----|
## **************************************************|
## 22:21:01 Writing NN index file to temp file /tmp/RtmpXcOcdQ/file55e95065c809
## 22:21:01 Searching Annoy index using 1 thread, search_k = 3000
## 22:21:03 Annoy recall = 100%
## 22:21:04 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
## 22:21:05 Initializing from normalized Laplacian + noise (using RSpectra)
## 22:21:05 Commencing optimization for 500 epochs, with 250324 positive edges
## 22:21:11 Optimization finished##
## excitatory_neurons2 inhibitory_neurons early_neurons excitatory_neurons1
## 5507 3732 3374 2290
## opc oligodendrocytes bipolar_neurons mature_neurons
## 1895 1767 1603 1394
## microglia astrocytes
## 973 589##
## 26wks 38wks
## 2954 2945
## Prediction/classification_results:## 0 1
## 1497 1419## Actual_classifications:##
## 0 1
## 1430 1486## Confusion Matrix and Statistics
##
## Reference
## Prediction 0 1
## 0 1181 316
## 1 249 1170
##
## Accuracy : 0.8062
## 95% CI : (0.7914, 0.8204)
## No Information Rate : 0.5096
## P-Value [Acc > NIR] : < 2.2e-16
##
## Kappa : 0.6127
##
## Mcnemar's Test P-Value : 0.005492
##
## Sensitivity : 0.7873
## Specificity : 0.8259
## Pos Pred Value : 0.8245
## Neg Pred Value : 0.7889
## Prevalence : 0.5096
## Detection Rate : 0.4012
## Detection Prevalence : 0.4866
## Balanced Accuracy : 0.8066
##
## 'Positive' Class : 1
## ## Setting levels: control = 0, case = 1## Warning in roc.default(response, predictor, auc = TRUE, ...): Deprecated use a
## matrix as predictor. Unexpected results may be produced, please pass a numeric
## vector.## Setting direction: controls < cases## Area under the curve: 0.8843## Length Class Mode
## call 6 -none- call
## response 2983 -none- numeric
## covariate 71592 -none- numeric
## model.list 2 -none- list
## err.fct 1 -none- function
## act.fct 1 -none- function
## linear.output 1 -none- logical
## data 21836 data.frame list
## exclude 0 -none- NULL
## net.result 1 -none- list
## weights 1 -none- list
## generalized.weights 1 -none- list
## startweights 1 -none- list
## result.matrix 768 -none- numeric
## Setting levels: control = 0, case = 1## Warning in roc.default(x, predictor, plot = TRUE, ...): Deprecated use a matrix
## as predictor. Unexpected results may be produced, please pass a numeric vector.## Setting direction: controls < cases
## PC_ 1
## Positive: RFX4, SLC1A3, ZBTB20, LRIG1, QKI, ZEB1, MMD2, SPARCL1, CHD7, ERBB4
## DOCK1, FBXL7, EEPD1, MSI2, TNC, NEAT1, NPAS3, CECR2, PARD3B, ITPR2
## FOXO1, CLU, RFTN2, CD9, HOPX, SLC4A4, PRDM16, SYNE2, MFGE8, TCF7L1
## Negative: CALN1, KLHL1, SCN9A, PCSK2, CCBE1, MYO16, SYN3, FGF13, PTCHD1-AS, XKR4
## DYNC1I1, NWD2, TENM1, GRM7, GRM1, FAM19A1, FRMD3, PPP2R2C, IQCJ-SCHIP1, FGF12
## PRR16, CACNA1E, AC060809.1, MIR137HG, CHRM2, PLPPR1, LINGO2, RYR3, MACROD2, C8orf34
## PC_ 2
## Positive: MMD2, RFX4, TNC, LRIG1, AC007402.1, SLC1A2, TFRC, CACHD1, SPON1, LINC00511
## RGMA, FOXO1, MSI2, EEPD1, ATP13A4, ARHGEF26, TIMP3, SLC4A4, SEMA5A, RNF219-AS1
## TCF7L1, SHROOM3, ITPR2, PARD3B, AC002429.2, MFGE8, PITPNC1, EYA2, TCF7L2, DTNA
## Negative: RBFOX1, TMSB10, SYT1, NKAIN2, MAP1B, ZNF536, SLC24A2, STMN2, GALNT17, FTH1
## CNTNAP2, CUX2, PCLO, VSNL1, MICAL2, DLGAP2, CELF4, KIAA1217, CALM3, CDH18
## NRGN, TENM2, PEX5L, EEF1A2, FTL, GRIN2B, SNRPN, ADARB2, CABP1, SPOCK3
## PC_ 3
## Positive: FAM19A1, IQCJ-SCHIP1, ARPP21, PTPRK, ANO3, DOK5, RALYL, CCBE1, FOXP1, KLHL1
## NWD2, DPYD, LDB2, CALN1, PTCHD1-AS, ACTN2, HS3ST2, RORB, NPY1R, UNC5C
## ITPR1, DYNC1I1, FMN1, RTN4RL1, RASGEF1C, NPNT, RYR2, NECAB1, NRGN, KCNH5
## Negative: NXPH1, GAD1, ERBB4, IGF1, DLX6-AS1, MAF, ZNF536, KCNIP1, DSCAML1, GRIP2
## GAD2, LHX6, NXPH2, ADARB2, ELFN1, DLX1, SYNPR, KIAA1217, MAGI1, LINC01322
## NPAS1, NETO2, LINC00854, PLS3, PTCHD4, AC233296.1, ARHGAP28, CACNG2, SNRPN, PAM
## PC_ 4
## Positive: HS3ST4, TRPM3, DLC1, GRIK3, KIAA1217, FAM160A1, SORCS1, TLE4, LINC02223, CDH18
## POU6F2, COL12A1, LRP1B, PEX5L, GABRG3, SLC35F3, LRRTM3, GSG1L, AL133346.1, SULF1
## FOXP2, ASTN2, TSHZ3, LINC01435, OLFM3, NEGR1, TMEM178A, OCA2, UNC13C, PTPRU
## Negative: CUX2, FAM19A1, MDGA1, PRSS12, CCBE1, SPON1, EPHA6, FGF13, EPHA3, UNC5D
## FAM19A2, CDH13, LINC00854, CDH4, PID1, PLXNA4, THBS1, NHSL1, ST8SIA2, IQCJ-SCHIP1
## SDK1, KITLG, PPFIBP1, NDST3, KIF26B, ARHGAP18, TENM4, PDZRN3, GRIA1, NECTIN3
## PC_ 5
## Positive: PTPRT, NXPH1, LHX6, SIAH3, PTCHD4, GRIN3A, PLCH1, MAF, GRIK1, SAMD5
## DLGAP2, AL033504.1, MARCH11, NXPH2, NTRK2, RASGRF2, TRHDE, MAFB, THSD4, TENM2
## ADCY8, KIAA1217, PTPRM, ST6GALNAC5, TRPC6, RELN, PAWR, MICAL2, NETO1, GRIP2
## Negative: DSCAM, ADARB2, PID1, LINC00854, SEMA3C, AC004158.1, PROX1, VCAN, MAML3, KITLG
## TRMT9B, SORCS3, KCNJ3, CHD7, ZNF804A, PALMD, NXN, GALNT13, ZBTB20, CECR2
## CDH4, NR2F2-AS1, SDK2, SYNE2, CHST11, DLX6-AS1, CNR1, ZFHX3, GAS2L3, ZEB1
## 22:22:45 UMAP embedding parameters a = 0.9922 b = 1.112
## 22:22:45 Read 5899 rows and found 15 numeric columns
## 22:22:45 Using Annoy for neighbor search, n_neighbors = 30
## 22:22:45 Building Annoy index with metric = cosine, n_trees = 50
## 0% 10 20 30 40 50 60 70 80 90 100%
## [----|----|----|----|----|----|----|----|----|----|
## **************************************************|
## 22:22:45 Writing NN index file to temp file /tmp/RtmpXcOcdQ/file55e922dcbdb2
## 22:22:45 Searching Annoy index using 1 thread, search_k = 3000
## 22:22:47 Annoy recall = 100%
## 22:22:47 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
## 22:22:49 Initializing from normalized Laplacian + noise (using RSpectra)
## 22:22:49 Commencing optimization for 500 epochs, with 233974 positive edges
## 22:22:54 Optimization finished##
## excitatory_neurons2 inhibitory_neurons early_neurons excitatory_neurons1
## 5507 3732 3374 2290
## opc oligodendrocytes bipolar_neurons mature_neurons
## 1895 1767 1603 1394
## microglia astrocytes
## 973 589##
## 28yrs 38wks
## 2803 2945## orig.ident nCount_RNA nFeature_RNA percent.mt
## AAACGAAAGCTAAGTA-1_5 38wks 1041 778 8.549472
## AAACGCTTCAAATGAG-1_5 38wks 1724 1180 3.654292
## AAACGCTTCCGTGGGT-1_5 38wks 18645 5228 3.657817
## AAAGAACTCTCCATAT-1_5 38wks 483 404 4.347826
## AAAGGATGTCACCACG-1_5 38wks 6507 2748 2.843092
## AAAGGATGTGCCTTTC-1_5 38wks 395 326 7.341772
## RNA_snn_res.0.05 seurat_clusters cell_types
## AAACGAAAGCTAAGTA-1_5 0 0 excitatory_neurons2
## AAACGCTTCAAATGAG-1_5 7 7 mature_neurons
## AAACGCTTCCGTGGGT-1_5 0 0 excitatory_neurons2
## AAAGAACTCTCCATAT-1_5 4 4 opc
## AAAGGATGTCACCACG-1_5 0 0 excitatory_neurons2
## AAAGGATGTGCCTTTC-1_5 2 2 early_neurons
## Prediction/classification_results:## 0 1
## 1566 1269## Actual_classifications:##
## 0 1
## 1425 1410## Confusion Matrix and Statistics
##
## Reference
## Prediction 0 1
## 0 1305 261
## 1 120 1149
##
## Accuracy : 0.8656
## 95% CI : (0.8525, 0.878)
## No Information Rate : 0.5026
## P-Value [Acc > NIR] : < 2.2e-16
##
## Kappa : 0.7311
##
## Mcnemar's Test P-Value : 7.368e-13
##
## Sensitivity : 0.8149
## Specificity : 0.9158
## Pos Pred Value : 0.9054
## Neg Pred Value : 0.8333
## Prevalence : 0.4974
## Detection Rate : 0.4053
## Detection Prevalence : 0.4476
## Balanced Accuracy : 0.8653
##
## 'Positive' Class : 1
## ## Setting levels: control = 0, case = 1## Warning in roc.default(response, predictor, auc = TRUE, ...): Deprecated use a
## matrix as predictor. Unexpected results may be produced, please pass a numeric
## vector.## Setting direction: controls < cases## Area under the curve: 0.9124## Length Class Mode
## call 6 -none- call
## response 2913 -none- numeric
## covariate 64086 -none- numeric
## model.list 2 -none- list
## err.fct 1 -none- function
## act.fct 1 -none- function
## linear.output 1 -none- logical
## data 21836 data.frame list
## exclude 0 -none- NULL
## net.result 1 -none- list
## weights 1 -none- list
## generalized.weights 1 -none- list
## startweights 1 -none- list
## result.matrix 728 -none- numeric
## Setting levels: control = 0, case = 1## Warning in roc.default(x, predictor, plot = TRUE, ...): Deprecated use a matrix
## as predictor. Unexpected results may be produced, please pass a numeric vector.## Setting direction: controls < cases
## PC_ 1
## Positive: SPP1, HHIP, CD9, CNP, GLUL, CRYAB, LPAR1, SLC1A3, TF, GPR37
## QKI, NEAT1, UGT8, OLIG1, MBP, COL4A5, DAAM2, DOCK1, DOCK5, BCAS1
## ZBTB20, ENPP2, RGCC, HTRA1, ST18, MT2A, TTYH2, DOCK10, CLMN, FGFR2
## Negative: DLGAP2, MIAT, RBFOX1, SYN3, OPCML, FGF12, GRIN2A, PPP2R2C, ERC2, AGBL4
## FRMPD4, CACNA1D, CHRM3, CELF4, GRIN2B, FGF14, GRM5, CADPS, RIMS2, MYRIP
## XKR4, SYBU, KCNIP4, ASIC2, CACNA2D3, SHISA9, RBFOX3, RYR2, PTPRR, MTUS2
## PC_ 2
## Positive: MAP1B, SYT1, NRGN, NEFL, ENC1, THY1, VSNL1, CCK, NEFM, PHYHIP
## VGF, TMSB10, CALM3, SNAP25, STMN2, RBFOX1, CHGA, TUBA1B, CREG2, CAMK2A
## CHGB, OLFM1, GABRA1, SLC17A7, PCSK1N, TUBB2A, DKK3, NPTX1, EEF1A2, YWHAH
## Negative: CD9, PDE4B, SPATA6, GLUL, GRAMD2B, DOCK1, QKI, HHIP, NEAT1, CDH20
## ARAP2, FBXL7, NPAS3, KANK1, HTRA1, CNP, FGFR2, SASH1, SLC1A3, ZBTB20
## AC002429.2, RFX4, PREX2, FOXO1, GPR37, FHIT, LRIG1, DOCK5, ATP13A4, LPAR1
## PC_ 3
## Positive: ITPR2, RFX4, MERTK, MMD2, APBB1IP, APOE, GPC5, DOCK8, RNF219-AS1, SLCO2B1
## PALD1, ADAM28, SLC1A2, RHBDF2, INPP5D, ARHGAP24, TBXAS1, AC002429.2, SLC7A11, ENTPD1
## PITPNC1, C3, ATP1A2, AQP4, AC008691.1, NHSL1, RREB1, CSGALNACT1, LRMDA, CACHD1
## Negative: HHIP, CNP, GPR37, CRYAB, TF, MBP, ENPP2, UGT8, CLMN, PALM2
## SPP1, ST18, LPAR1, EDIL3, BCAS1, CTNNA3, OLIG1, SYNJ2, RGCC, RNF220
## LINC01630, LINC01170, FAM107B, SLC24A2, SLC22A15, COL4A5, SPOCK3, KCNH8, SVEP1, RAPGEF5
## PC_ 4
## Positive: APBB1IP, DOCK8, ADAM28, SLCO2B1, RHBDF2, INPP5D, TBXAS1, AC008691.1, C3, PALD1
## LPCAT2, CSF2RA, RCSD1, DOCK2, FYB1, A2M, ARHGAP25, LRMDA, LRRK1, SP100
## FLI1, CPED1, AOAH, MYO1F, CARD11, PLXDC2, SYNDIG1, DENND3, SKAP2, ARHGAP22
## Negative: MMD2, RFX4, GPC5, SLC1A2, RNF219-AS1, PITPNC1, TNC, CACHD1, ATP1A2, AC002429.2
## SLC4A4, CTNNA2, SLC7A11, NKAIN3, NPAS3, ATP13A4, RORA, RGMA, PTPRZ1, AQP4
## SPON1, LINC00511, ADGRV1, FGFR3, TFRC, SHROOM3, PARD3, ACSBG1, ARHGEF26, EYA2
## PC_ 5
## Positive: SPARCL1, CLU, CCK, CREG2, THY1, GABRA1, DKK3, SNAP25, CAMK2A, VGF
## CHGA, VSNL1, PHYHIP, CHN1, PCSK1N, NEFL, NPTX1, OLFM1, SERPINI1, CHGB
## CABP1, HTR2A, MAL2, SV2B, DIRAS2, NRGN, ENC1, C11orf87, GABRB2, VSTM2A
## Negative: PLPPR1, PTPRD, KLHL1, CALN1, FRMD4A, SLC24A3, SYN3, ABI3BP, LUZP2, LIMS2
## RASGEF1C, KIAA1211, DAB1, LDLRAD4, FRMD3, MIAT, ST8SIA2, PLXNA4, FGF13, ROBO2
## MARCH1, KIRREL3, SEMA6D, XKR4, CCBE1, MYO16, ANKRD30BL, SCN9A, DOK5, SLC44A5
## 22:24:35 UMAP embedding parameters a = 0.9922 b = 1.112
## 22:24:35 Read 5748 rows and found 15 numeric columns
## 22:24:35 Using Annoy for neighbor search, n_neighbors = 30
## 22:24:35 Building Annoy index with metric = cosine, n_trees = 50
## 0% 10 20 30 40 50 60 70 80 90 100%
## [----|----|----|----|----|----|----|----|----|----|
## **************************************************|
## 22:24:35 Writing NN index file to temp file /tmp/RtmpXcOcdQ/file55e914a3a657
## 22:24:35 Searching Annoy index using 1 thread, search_k = 3000
## 22:24:37 Annoy recall = 100%
## 22:24:38 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
## 22:24:39 Initializing from normalized Laplacian + noise (using RSpectra)
## 22:24:39 Commencing optimization for 500 epochs, with 235384 positive edges
## 22:24:45 Optimization finished##
## excitatory_neurons2 inhibitory_neurons early_neurons excitatory_neurons1
## 5507 3732 3374 2290
## opc oligodendrocytes bipolar_neurons mature_neurons
## 1895 1767 1603 1394
## microglia astrocytes
## 973 589##
## 28yrs 45yrs
## 2803 2701## orig.ident nCount_RNA nFeature_RNA percent.mt
## AAACCCAAGGATACGC-1_6 28yrs 881 593 15.4370034
## AAACCCAAGTTGGCTT-1_6 28yrs 384 308 12.7604167
## AAACCCAGTTGCTCAA-1_6 28yrs 277 246 3.6101083
## AAACGAAGTTACCTTT-1_6 28yrs 333 302 0.6006006
## AAACGAATCGAGTTGT-1_6 28yrs 285 224 14.7368421
## AAACGCTGTGGTCTCG-1_6 28yrs 5857 2537 1.5024757
## RNA_snn_res.0.05 seurat_clusters cell_types
## AAACCCAAGGATACGC-1_6 5 5 oligodendrocytes
## AAACCCAAGTTGGCTT-1_6 6 6 bipolar_neurons
## AAACCCAGTTGCTCAA-1_6 6 6 bipolar_neurons
## AAACGAAGTTACCTTT-1_6 8 8 microglia
## AAACGAATCGAGTTGT-1_6 6 6 bipolar_neurons
## AAACGCTGTGGTCTCG-1_6 5 5 oligodendrocytes## AAACCCAAGGATACGC-1_6 AAACCCAAGTTGGCTT-1_6 AAACCCAGTTGCTCAA-1_6
## 28yrs 28yrs 28yrs
## AAACGAAGTTACCTTT-1_6 AAACGAATCGAGTTGT-1_6 AAACGCTGTGGTCTCG-1_6
## 28yrs 28yrs 28yrs
## Levels: 28yrs 45yrs
## Prediction/classification_results:## 0 1
## 1289 1418## Actual_classifications:##
## 0 1
## 1349 1358## Confusion Matrix and Statistics
##
## Reference
## Prediction 0 1
## 0 1214 75
## 1 135 1283
##
## Accuracy : 0.9224
## 95% CI : (0.9117, 0.9322)
## No Information Rate : 0.5017
## P-Value [Acc > NIR] : < 2.2e-16
##
## Kappa : 0.8448
##
## Mcnemar's Test P-Value : 4.673e-05
##
## Sensitivity : 0.9448
## Specificity : 0.8999
## Pos Pred Value : 0.9048
## Neg Pred Value : 0.9418
## Prevalence : 0.5017
## Detection Rate : 0.4740
## Detection Prevalence : 0.5238
## Balanced Accuracy : 0.9223
##
## 'Positive' Class : 1
## ## Setting levels: control = 0, case = 1## Warning in roc.default(response, predictor, auc = TRUE, ...): Deprecated use a
## matrix as predictor. Unexpected results may be produced, please pass a numeric
## vector.## Setting direction: controls < cases## Area under the curve: 0.9465## Length Class Mode
## call 6 -none- call
## response 2797 -none- numeric
## covariate 53143 -none- numeric
## model.list 2 -none- list
## err.fct 1 -none- function
## act.fct 1 -none- function
## linear.output 1 -none- logical
## data 21836 data.frame list
## exclude 0 -none- NULL
## net.result 1 -none- list
## weights 1 -none- list
## generalized.weights 1 -none- list
## startweights 1 -none- list
## result.matrix 668 -none- numeric
## Setting levels: control = 0, case = 1## Warning in roc.default(x, predictor, plot = TRUE, ...): Deprecated use a matrix
## as predictor. Unexpected results may be produced, please pass a numeric vector.## Setting direction: controls < cases
## PC_ 1
## Positive: ST18, CLMN, ENPP2, DOCK5, TF, RNF220, NEAT1, SLC5A11, DOCK10, FA2H
## CDK18, CTNNA3, MBP, CRYAB, UGT8, BCAS1, TTYH2, HHIP, LINC00609, SPP1
## CNP, DAAM2, CERCAM, LPAR1, ATP10B, GLUL, PLD1, FAM107B, DOCK1, FRMD4B
## Negative: STXBP5L, AGBL4, MTUS2, RBFOX1, KSR2, CABP1, DLGAP2, CDH18, FGF14, AL117329.1
## CSMD1, KCNIP4, RIMS2, SYT1, ATRNL1, FSTL4, GABRB2, OPCML, FRMPD4, CHRM3
## GRM5, ASIC2, OLFM3, GRIN2A, KCNQ5, DGKB, STXBP5-AS1, LRRTM4, LRFN5, HCN1
## PC_ 2
## Positive: MAP1B, ROBO2, SYT1, STMN2, TMSB10, SOX4, FGF13, ST8SIA2, KIAA1211, KCNH7
## EPHA3, CCBE1, ENC1, IGF2BP2, SYNE2, CLMP, RBFOX1, DCLK1, GAP43, NNAT
## NEFL, NEFM, FABP7, EPHA5, SLC44A5, DLX6-AS1, GRIP1, KLHL1, PGM2L1, NREP
## Negative: HPSE2, CDH20, NEAT1, HIF3A, ZNF98, CABLES1, RANBP3L, ATP1A2, ITPKB, COL5A3
## DGKG, FHIT, ALDH1L1, IL17RB, PREX2, ACOT11, PDE7B, GRAMD2B, GNA14, GJA1
## NEBL, GLUL, GPC5, RNF219-AS1, SASH1, DTNA, GFAP, BAG3, GLIS3, PAPLN
## PC_ 3
## Positive: ST18, ENPP2, CTNNA3, CLMN, TF, MBP, RNF220, SLC24A2, SLC5A11, CDK18
## HHIP, FA2H, UGT8, EDIL3, AK5, BCAS1, PDE1C, PPM1H, RAPGEF5, DOCK10
## CNP, SPOCK3, PPP1R16B, CERCAM, PEX5L, PLD1, DOCK5, PCSK6, PLCL1, PALM2
## Negative: HPSE2, ARHGAP24, RANBP3L, ATP1A2, HIF3A, GJA1, ALDH1L1, RNF219-AS1, GFAP, SLC1A2
## MERTK, AQP4, SLC7A11, COL5A3, CABLES1, APOE, PITPNC1, PAPLN, SLC39A12, GPC5
## GNA14, ZNF98, GLIS3, F3, FAM189A2, PARD3, RFX4, FGFR3, PRDM16, BMPR1B
## PC_ 4
## Positive: ERBB4, NKAIN3, LSAMP, SLC1A2, HIF3A, ROBO2, CTNNA2, PARD3, NRG3, PTPRD
## NPAS3, PTPRZ1, ATP1A2, HPSE2, AL589740.1, ADGRV1, MAGI2, PITPNC1, KIAA1211, NFIA
## LINC00511, FBXL7, ALDH1L1, MEIS2, RANBP3L, RYR3, PREX2, GFAP, RNF219-AS1, ADGRL3
## Negative: APBB1IP, DOCK8, ADAM28, RHBDF2, C3, TBXAS1, SLCO2B1, FYB1, PALD1, INPP5D
## DOCK2, SP100, LRMDA, AC074327.1, ATP8B4, LPCAT2, AC008691.1, RCSD1, ARHGAP25, RUNX1
## PIK3AP1, FLI1, DENND3, MYO1F, RBM47, A2M, AOAH, CPED1, HCK, LRRK1
## PC_ 5
## Positive: CLU, SPARCL1, NRGN, CCK, HPSE2, DKK3, CHN1, CREG2, GJA1, RANBP3L
## CAMK2A, VSNL1, PHYHIP, AQP4, SV2B, GNA14, NEFL, GPC5, THY1, PAMR1
## GABRA1, RNF219-AS1, ITPKB, FAM107A, GFAP, ENC1, GLIS3, NECAB1, SLC39A12, GLUL
## Negative: AC004852.2, MEGF11, FERMT1, PCDH15, STK32A, LHFPL3, CSPG4, SMOC1, TMEM132C, SEMA5A
## CACNG5, GRIK1, DISC1, AFAP1L2, MYT1, ALK, MIR3681HG, ITGA8, PLPP4, VCAN
## AL445250.1, LUZP2, NXPH1, DSCAM, COL9A1, PDGFRA, TEK, CHST9, CHST11, GRID2
## 22:26:03 UMAP embedding parameters a = 0.9922 b = 1.112
## 22:26:03 Read 5504 rows and found 15 numeric columns
## 22:26:03 Using Annoy for neighbor search, n_neighbors = 30
## 22:26:03 Building Annoy index with metric = cosine, n_trees = 50
## 0% 10 20 30 40 50 60 70 80 90 100%
## [----|----|----|----|----|----|----|----|----|----|
## **************************************************|
## 22:26:03 Writing NN index file to temp file /tmp/RtmpXcOcdQ/file55e945f11c85
## 22:26:03 Searching Annoy index using 1 thread, search_k = 3000
## 22:26:04 Annoy recall = 100%
## 22:26:05 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
## 22:26:07 Initializing from normalized Laplacian + noise (using RSpectra)
## 22:26:07 Commencing optimization for 500 epochs, with 225422 positive edges
## 22:26:12 Optimization finished##
## excitatory_neurons2 inhibitory_neurons early_neurons excitatory_neurons1
## 5507 3732 3374 2290
## opc oligodendrocytes bipolar_neurons mature_neurons
## 1895 1767 1603 1394
## microglia astrocytes
## 973 589##
## 45yrs 53yrs
## 2701 2819## orig.ident nCount_RNA nFeature_RNA percent.mt
## AAACCCACAGCCCACA-1_7 45yrs 2712 1450 2.6917404
## AAACCCAGTGATCATC-1_7 45yrs 1113 748 0.9883199
## AAACCCAGTGTTGATC-1_7 45yrs 2539 1353 3.4265459
## AAACCCAGTTGGGTTT-1_7 45yrs 8475 3164 0.3539823
## AAACCCATCCCTTGGT-1_7 45yrs 10934 3871 5.4691787
## AAACGAAAGTTTCGAC-1_7 45yrs 8511 3085 5.0875338
## RNA_snn_res.0.05 seurat_clusters cell_types
## AAACCCACAGCCCACA-1_7 9 9 astrocytes
## AAACCCAGTGATCATC-1_7 4 4 opc
## AAACCCAGTGTTGATC-1_7 9 9 astrocytes
## AAACCCAGTTGGGTTT-1_7 4 4 opc
## AAACCCATCCCTTGGT-1_7 3 3 excitatory_neurons1
## AAACGAAAGTTTCGAC-1_7 3 3 excitatory_neurons1
## Prediction/classification_results:## 0 1
## 1665 1049## Actual_classifications:##
## 0 1
## 1314 1400## Confusion Matrix and Statistics
##
## Reference
## Prediction 0 1
## 0 1194 471
## 1 120 929
##
## Accuracy : 0.7822
## 95% CI : (0.7662, 0.7976)
## No Information Rate : 0.5158
## P-Value [Acc > NIR] : < 2.2e-16
##
## Kappa : 0.5676
##
## Mcnemar's Test P-Value : < 2.2e-16
##
## Sensitivity : 0.6636
## Specificity : 0.9087
## Pos Pred Value : 0.8856
## Neg Pred Value : 0.7171
## Prevalence : 0.5158
## Detection Rate : 0.3423
## Detection Prevalence : 0.3865
## Balanced Accuracy : 0.7861
##
## 'Positive' Class : 1
## ## Setting levels: control = 0, case = 1## Warning in roc.default(response, predictor, auc = TRUE, ...): Deprecated use a
## matrix as predictor. Unexpected results may be produced, please pass a numeric
## vector.## Setting direction: controls < cases## Area under the curve: 0.8198## Length Class Mode
## call 6 -none- call
## response 2806 -none- numeric
## covariate 28060 -none- numeric
## model.list 2 -none- list
## err.fct 1 -none- function
## act.fct 1 -none- function
## linear.output 1 -none- logical
## data 21836 data.frame list
## exclude 0 -none- NULL
## net.result 1 -none- list
## weights 1 -none- list
## generalized.weights 1 -none- list
## startweights 1 -none- list
## result.matrix 488 -none- numeric
## Setting levels: control = 0, case = 1## Warning in roc.default(x, predictor, plot = TRUE, ...): Deprecated use a matrix
## as predictor. Unexpected results may be produced, please pass a numeric vector.## Setting direction: controls < cases
## PC_ 1
## Positive: AL117329.1, STXBP5L, CABP1, LINC01250, AGBL4, FSTL4, NIPAL2, KSR2, CDH18, CAMK2A
## SLC22A10, AC067956.1, DLGAP2, MTUS2, KCNIP4, FMN1, AC011287.1, ZMAT4, SLC35F3, CBLN2
## RYR2, DGKB, GRIN2A, ASIC2, OLFM3, GABRB2, NRGN, PHYHIP, HTR1E, KCNQ5
## Negative: ST18, RNF220, CLMN, ENPP2, NEAT1, FA2H, QKI, DOCK10, TF, SLC5A11
## FRMD4B, CTNNA3, CERCAM, CDK18, DAAM2, BCAS1, DOCK1, TTYH2, LINC00609, PCSK6
## ATP10B, FAM107B, ZBTB20, UGT8, PREX1, KCNH8, PIEZO2, MBP, RFTN2, FBXL7
## PC_ 2
## Positive: ROBO2, MAP1B, STMN2, SYT1, RBFOX1, KCNH7, DCLK1, TMSB10, FGF13, SOX4
## GRIP1, KIAA1211, SLC44A5, GRIA1, FRMD4A, UNC5D, CCBE1, EPHA5, ST8SIA2, EPHA3
## CLMP, LINC01122, PTPRO, PLXNA4, C8orf34, KCNB2, IGF2BP2, NREP, DLX6-AS1, NELL2
## Negative: CDH20, NEAT1, HPSE2, IL17RB, FHIT, BAG3, COBL, ATP10B, COL5A3, ITPKB
## HIF3A, DGKG, CABLES1, ZNF98, DOCK1, KANK1, GFAP, ALDH1L1, FKBP5, HSPB1
## SASH1, PDE7B, SLC9A9, GRAMD2B, DNAJA4, RANBP3L, LMCD1-AS1, ATP1A2, GNA14, BCAS1
## PC_ 3
## Positive: HPSE2, GFAP, HIF3A, ALDH1L1, ATP1A2, COL5A3, SLC1A2, RANBP3L, PITPNC1, CABLES1
## ZNF98, RNF219-AS1, PARD3, GNA14, FAM107A, GJA1, RFX4, IGFBP7, RYR3, ARHGAP24
## SLC7A11, SLC39A12, EYA2, PAMR1, PRDM16, F3, GLIS3, FAM189A2, COLEC12, RGS20
## Negative: ST18, RNF220, CDK18, CTNNA3, CLMN, MBP, ENPP2, CERCAM, TF, SLC5A11
## FA2H, SLC24A2, PCSK6, DOCK10, PDE1C, AK5, PIEZO2, MAN2A1, PLD1, POLR2F
## EDIL3, PLCL1, UGT8, ELMO1, BCAS1, PEX5L, KIF6, SPOCK3, LINC00609, PALM2
## PC_ 4
## Positive: HPSE2, NEAT1, GFAP, RANBP3L, ITPKB, ARHGAP24, GNA14, COL5A3, RNF219-AS1, GLIS3
## ARHGAP26, GJA1, FAM107A, PAMR1, COLEC12, FAM189A2, ACSBG1, SLC39A12, SLC39A11, GRIN2C
## ZNF98, CLU, SLC7A11, IQCA1, AQP4, PAPLN, RGS20, IGFBP7, RYR3, APOE
## Negative: AC004852.2, PCDH15, ITGA8, LHFPL3, CSPG4, CRISPLD2, MIR3681HG, SMOC1, FERMT1, CACNG5
## BEST3, TMEM132C, GRIK1, SEMA5A, PLPP4, MYT1, AFAP1L2, ALK, PDGFRA, CHST9
## AL445250.1, CALCRL, NXPH1, PRRX1, C1QL1, CA10, GALNT13, TEK, NOS1, VCAN
## PC_ 5
## Positive: RUNX1, FYB1, AC074327.1, LRMDA, TBXAS1, ADAM28, SP100, APBB1IP, DOCK2, PIK3AP1
## C3, CCDC26, INPP5D, RBM47, SLCO2B1, RHBDF2, LYN, ARHGAP15, AOAH, RCSD1
## ARHGAP24, MYO1F, FLI1, ATP8B4, PALD1, ARHGAP6, TGFBR2, SRGN, ARHGAP25, FAM129A
## Negative: MAGI2, GFAP, LSAMP, NRG3, CTNNA2, NPAS3, ERBB4, PTPRD, MAP1B, SLC1A2
## ALDH1L1, RANBP3L, GJA1, ROBO2, LIMCH1, COL5A3, HPSE2, RYR3, ATP1A2, ADGRV1
## FAM189A2, ACSBG1, FBXL7, SLC25A18, NKAIN2, CLU, FAM107A, NTRK2, PRDM16, AQP4
## 22:28:00 UMAP embedding parameters a = 0.9922 b = 1.112
## 22:28:00 Read 5520 rows and found 15 numeric columns
## 22:28:00 Using Annoy for neighbor search, n_neighbors = 30
## 22:28:00 Building Annoy index with metric = cosine, n_trees = 50
## 0% 10 20 30 40 50 60 70 80 90 100%
## [----|----|----|----|----|----|----|----|----|----|
## **************************************************|
## 22:28:01 Writing NN index file to temp file /tmp/RtmpXcOcdQ/file55e92da5d860
## 22:28:01 Searching Annoy index using 1 thread, search_k = 3000
## 22:28:02 Annoy recall = 100%
## 22:28:03 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
## 22:28:05 Initializing from normalized Laplacian + noise (using RSpectra)
## 22:28:05 Commencing optimization for 500 epochs, with 228224 positive edges
## 22:28:10 Optimization finishedHeatmapped ordered list of early to late developmental genes from top to bottom determined by stage-wise neural network predictive classifications.
##
## 17wks 20wks 22wks 26wks 28yrs 38wks 45yrs 53yrs
## 2996 2912 2994 2954 2803 2945 2701 2819
Heatmapped ordered list of early to late developmental genes from top to bottom determined by annotated cell types.
R version 4.4.1 (2024-06-14) – “Race for Your Life” Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu
RStudio 2024.04.2+764 “Chocolate Cosmos” Release (e4392fc9ddc21961fd1d0efd47484b43f07a4177, 2024-06-05) for Ubuntu Jammy Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) rstudio/2024.04.2+764 Chrome/120.0.6099.291 Electron/28.3.1 Safari/537.36, Quarto 1.4.555