dxsmall_analysis
Mao Ding
2023-06-12
Objective
Perform real world data analysis using BifurcatoR tools to check bimodality
dxsmall data: pediatric leukemia gene expression values with different fusion groups
## class: SingleCellExperiment
## dim: 6 470
## metadata(0):
## assays(2): counts logcounts
## rownames(6): MECOM PRDM16 ... NCAM1 KDM5D
## rowData names(4): gene_id medianLogCounts rangeLogCounts madLogCounts
## colnames(470): PAEAKL PAECCE ... PAYFYN PAYIET
## colData names(8): AgeGroup Sex ... OS OSIFirst 10 columns of counts
## PAEAKL PAECCE PAKLPD PAKTCX PANGDN PANPSV PANTCT PANTRL PANTWV PANVUF
## MECOM 2 5 6 8639 7992 1525 47 0 2361 2277
## PRDM16 16 3 3 18 25 2 17 2 13 15
## CD33 3969 3304 1825 2808 3913 3146 2256 1146 1030 839
## CD34 42 27571 39 2072 5201 15 202 8 5896 431
## NCAM1 29383 260 1062 16 90 2 4670 95 0 0
## KDM5D 1 5694 3 15 6730 5916 3583 1 4 8Summary Statistics of dxsmall counts
## MECOM PRDM16 CD33 CD34
## Min. : 0 Min. : 0.00 Min. : 18.0 Min. : 2.0
## 1st Qu.: 1 1st Qu.: 4.00 1st Qu.: 704.5 1st Qu.: 29.0
## Median : 6 Median : 10.00 Median : 1431.0 Median : 179.5
## Mean : 1666 Mean : 781.92 Mean : 1839.8 Mean : 2796.5
## 3rd Qu.: 50 3rd Qu.: 73.25 3rd Qu.: 2547.5 3rd Qu.: 3714.0
## Max. :30144 Max. :8134.00 Max. :11016.0 Max. :35040.0
## NCAM1 KDM5D
## Min. : 0.0 Min. : 0
## 1st Qu.: 15.0 1st Qu.: 3
## Median : 54.0 Median : 1492
## Mean : 888.6 Mean : 3501
## 3rd Qu.: 456.0 3rd Qu.: 5829
## Max. :29383.0 Max. :61745First 10 columns of logcounts
## PAEAKL PAECCE PAKLPD PAKTCX PANGDN PANPSV PANTCT
## MECOM 1.1437896 2.159773 2.202325 12.635797 12.166000 9.918715 4.920319
## PRDM16 3.4164146 1.623430 1.485994 3.833752 3.942245 1.181463 3.534913
## CD33 11.2296987 11.162989 10.098914 11.014947 11.136046 10.962656 10.457859
## CD34 4.7225611 14.223301 4.609656 10.576675 11.546401 3.393759 6.986912
## NCAM1 14.1173132 7.502706 9.318746 3.676419 5.720816 1.181463 11.506984
## KDM5D 0.6823965 11.947954 1.485994 3.590813 11.918109 11.873421 11.124880
## PANTRL PANTWV PANVUF
## MECOM 0.000000 10.507923 10.643734
## PRDM16 1.942100 3.171871 3.527659
## CD33 10.670511 9.312449 9.204888
## CD34 3.628841 11.827667 8.246217
## NCAM1 7.087735 0.000000 0.000000
## KDM5D 1.275795 1.792971 2.726274Summary Statistics of dxsmall logcounts
## MECOM PRDM16 CD33 CD34
## Min. : 0.000 Min. : 0.000 Min. : 4.253 Min. : 1.484
## 1st Qu.: 1.238 1st Qu.: 2.222 1st Qu.: 9.485 1st Qu.: 4.856
## Median : 2.653 Median : 3.357 Median :10.445 Median : 7.565
## Mean : 4.417 Mean : 4.787 Mean :10.144 Mean : 8.085
## 3rd Qu.: 5.521 3rd Qu.: 6.077 3rd Qu.:11.090 3rd Qu.:11.559
## Max. :14.512 Max. :12.697 Max. :12.681 Max. :14.593
## NCAM1 KDM5D
## Min. : 0.000 Min. : 0.000
## 1st Qu.: 3.751 1st Qu.: 1.873
## Median : 5.782 Median :11.124
## Mean : 6.329 Mean : 7.450
## 3rd Qu.: 8.808 3rd Qu.:12.276
## Max. :14.117 Max. :15.161rowData: Rows contains their own metadata as a dataframe format to describe their features.
## DataFrame with 6 rows and 4 columns
## gene_id medianLogCounts rangeLogCounts madLogCounts
## <character> <numeric> <numeric> <numeric>
## MECOM ENSG00000085276.19 1.83653 14.5121 2.44570
## PRDM16 ENSG00000142611.17 3.32100 12.6973 2.85342
## CD33 ENSG00000105383.15 10.05794 9.9846 1.41178
## CD34 ENSG00000174059.17 10.86344 16.0191 3.86343
## NCAM1 ENSG00000149294.17 4.93129 15.8618 3.14829
## KDM5D ENSG00000012817.16 7.56726 15.1607 7.56651colData: Columns contains their own metadata as a dataframe format to describe their features.
## DataFrame with 470 rows and 8 columns
## AgeGroup Sex FAB BlastPercent fusion FusionGroup
## <factor> <factor> <factor> <numeric> <factor> <factor>
## PAEAKL Child Female M4 NA KMT2A-MLLT1 MLL
## PAECCE Infant Male M4 NA KMT2A-MLLT10 MLL
## PAKLPD Infant Female M4 NA KMT2A-ELL MLL
## PAKTCX Child Female M4 NA KMT2A-ELL MLL
## PANGDN AYA Male M4 NA KMT2A-MLLT4 MLL
## ... ... ... ... ... ... ...
## PAYBSY AYA Female M5 NA NUP98-NSD1 NSD1
## PAYDUC AYA Female M5 NA NUP98-NSD1 NSD1
## PAYETG Child Female NA NA NUP98-NSD1 NSD1
## PAYFYN Child Male NA NA NUP98-NSD1 NSD1
## PAYIET Child Male M1 NA NUP98-NSD1 NSD1
## OS OSI
## <numeric> <numeric>
## PAEAKL 163 1
## PAECCE 147 1
## PAKLPD 2707 0
## PAKTCX 1896 1
## PANGDN 3063 0
## ... ... ...
## PAYBSY 763 1
## PAYDUC 420 1
## PAYETG NA 0
## PAYFYN NA 0
## PAYIET 577 1Age Group
Gender
Fusion Group
Density Plot of MECOM logcounts in different fusion group
Mclust fit: fitting the dataset using a mixture model based on the hypothesis that two clusters exist by specifying group number equals 2.
mclust fit object density plot in MLL
## [1] "Mean of the two clusters in MLL are: 2.55259783079578 12.2014398882966"## [1] "SD of the two clusters in MLL are: 1.7339533318677 1.2803192180987"## [1] "Mixing proportion of the two clusters in MLL are: 0.713896457765668 0.286103542234332"Classification for Each cell in MLL
## PAEAKL PAECCE PAKLPD PAKTCX PANGDN PANPSV PANTCT PANTRL PANTWV PANVUF PANXWX
## 1 1 1 2 2 2 1 1 2 2 2
## PAPAJE PAPWZR PAPXAZ PAPZTC PARAEF PARBIU PARBRA PARBXE PARDDY
## 1 2 1 2 1 1 1 1 1