Input data format
SPARKLE supports multiple input formats. Users can directly input single-cell Seurat objects,Seurat metadata, or dataframes with calculated cell proportions.
Input formats 1: Seurat objects
library(SPARKLE)
seurat_object <-MNP.seurat_object
class(seurat_object)## [1] "Seurat"
## attr(,"package")
## [1] "SeuratObject"sparkle.data <- cwas_build_model_data(inputdata = seurat_object,Sample = "Patient.No",Phenotype = "Status",Celltype ="Clusters",Group ="Tissue",Subgroup = "Study.No",Control_label = "Healthy",Disease_label = "Cancer") ## [1] "Warning: No Covariate1 infomation"
## [1] "Warning: No Covariate2 infomation"
## [1] "No gene infomation added"
## [1] "No geneset score infomation added"Input formats 2: Seurat metadata
metadata <-MNP.metadata
knitr::kable(head(metadata), caption = "Seurat metadata") | orig.ident | nCount_RNA | nFeature_RNA | Initial.No | Study.No | Ascites.1_Blood.2_Breast.3_Colon.4_Stomach.5_Kidney.6_Liver.7_Lung.8_Pancreas.9_Skin.10_Spleen.11_Tonsil.12 | Patient.No | MirgDC.1_DC1.2_DC2.3_MacroMono.4 | Study | Tissue | Status | Clusters.NO | Clusters | nCount_integrated | nFeature_integrated | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ACTTGTTCACCGCTAG.1_1 | SeuratProject | 1628.662 | 719 | 1 | 1 | 1 | 1 | 3 | Tang-Huau | Ascites | Healthy | 6 | T cell doublets | 337.7403 | 1387 |
| ATTGGACCATGTCCTC.1_1 | SeuratProject | 1028.799 | 342 | 2 | 1 | 1 | 1 | 3 | Tang-Huau | Ascites | Healthy | 6 | T cell doublets | 262.4473 | 1390 |
| CCTTACGTCCCTGACT.1_1 | SeuratProject | 1779.581 | 959 | 3 | 1 | 1 | 1 | 3 | Tang-Huau | Ascites | Healthy | 6 | T cell doublets | 332.5596 | 1415 |
| TGTTCCGCAGAAGCAC.1_1 | SeuratProject | 1493.055 | 578 | 4 | 1 | 1 | 1 | 1 | Tang-Huau | Ascites | Healthy | 6 | T cell doublets | 350.6807 | 1364 |
| TTGACTTGTACTCAAC.1_1 | SeuratProject | 1555.572 | 806 | 5 | 1 | 1 | 1 | 1 | Tang-Huau | Ascites | Healthy | 6 | T cell doublets | 320.1611 | 1435 |
| AACTCAGGTAAGTGGC.2_1 | SeuratProject | 1460.183 | 767 | 6 | 1 | 1 | 1 | 3 | Tang-Huau | Ascites | Healthy | 6 | T cell doublets | 334.7708 | 1478 |
sparkle.data <- cwas_build_model_data(inputdata = metadata,Sample = "Patient.No",Phenotype = "Status",Celltype ="Clusters",Group ="Tissue",Subgroup = "Study.No",Control_label = "Healthy",Disease_label = "Cancer")## [1] "Warning: No Covariate1 infomation"
## [1] "Warning: No Covariate2 infomation"
## [1] "No gene infomation added"
## [1] "No geneset score infomation added"Input formats 3: data frame with cell rate information
covid.data.ratio <-SPARKLE::covid.data
knitr::kable(head(covid.data.ratio) , caption = "Cell rate information table") | sampleID | celltype | cellratio | dataset | tissue | severity |
|---|---|---|---|---|---|
| S-HC001 | NK | 0.0050188 | Batch08 | CD3+ T cell and CD19+ B cell sorted from fresh PBMC (FACS) | control |
| S-HC001 | CD8 | 0.4382343 | Batch08 | CD3+ T cell and CD19+ B cell sorted from fresh PBMC (FACS) | control |
| S-HC001 | B | 0.0929622 | Batch08 | CD3+ T cell and CD19+ B cell sorted from fresh PBMC (FACS) | control |
| S-HC001 | Mega | 0.0018250 | Batch08 | CD3+ T cell and CD19+ B cell sorted from fresh PBMC (FACS) | control |
| S-HC001 | Plasma | 0.0007984 | Batch08 | CD3+ T cell and CD19+ B cell sorted from fresh PBMC (FACS) | control |
| S-HC001 | CD4 | 0.4458766 | Batch08 | CD3+ T cell and CD19+ B cell sorted from fresh PBMC (FACS) | control |
sparkle.data <- cwas_build_model_data(inputdata = covid.data.ratio,Sample = "sampleID",Phenotype = "severity",Celltype ="celltype",Group ="tissue",Subgroup = "dataset",Control_label = "control",Disease_label = "severe/critical",Cellrate ="cellratio" )## [1] "Warning: No Covariate1 infomation"
## [1] "Warning: No Covariate2 infomation"
## [1] "No gene infomation added"
## [1] "No geneset score infomation added"