Pathway_pcascore_run
Pathway_pcascore_run.RdThe function can calculate the pathway pcascore for celltypes and single cells.
Usage
Pathway_pcascore_run(
Pagwas = NULL,
Pathway_list = NULL,
min.pathway.size = 10,
max.pathway.size = 1000
)Arguments
- Pagwas
Pagwas format
- Pathway_list
Pathawy gene list(gene symbol),list name is pathway name.
- min.pathway.size
Threshold for min pathway gene size.
- max.pathway.size
Threshold for max pathway gene size.
Examples
library(scPagwas)
Pagwas <- list()
# Start to read the single cell data
Single_data <- readRDS(system.file("extdata", "scRNAexample.rds",
package = "scPagwas"
))
Pagwas <- Single_data_input(
Pagwas = Pagwas,
assay = "RNA",
Single_data = Single_data,
Pathway_list = Genes_by_pathway_kegg
)
#> Input single cell data!
#> 10 cell types are remain, after filter!
Single_data <- Single_data[, colnames(Pagwas$data_mat)]
# Run pathway pca score!
Pagwas <- Pathway_pcascore_run(
Pagwas = Pagwas,
Pathway_list = Genes_by_pathway_kegg
)
#> * Start to get Pathway SVD socre!
#>
|
| | 0%
|
|======= | 10%[1] "Celltype1"
#>
|
|============== | 20%[1] "Celltype2"
#>
|
|===================== | 30%[1] "Celltype3"
#>
|
|============================ | 40%[1] "Celltype4"
#>
|
|=================================== | 50%[1] "Celltype5"
#>
|
|========================================== | 60%[1] "Celltype6"
#>
|
|================================================= | 70%[1] "Celltype7"
#>
|
|======================================================== | 80%[1] "Celltype8"
#>
|
|=============================================================== | 90%[1] "Celltype9"
#>
|
|======================================================================| 100%[1] "Celltype10"
#>
#> Using score as value column: use value.var to override.