takes files with positive and negative markers, as described in garnett, and returns list of markers

Usage

file_marker_parse(filename)

Arguments

filename: txt file to load

Value

list of positive and negative gene markers

Examples

marker_file <- system.file(
    "extdata",
    "hsPBMC_markers.txt",
    package = "clustifyr"
)

file_marker_parse(marker_file)
#> $pos
#> $pos$`CD34+`
#> [1] "CD34"   "THY1"   "ENG"    "KIT"    "PROM1 "
#> 
#> $pos$`NK cells`
#> [1] "NCAM1"  "FCGR3A"
#> 
#> $pos$Monocytes
#> [1] "CD14"    "FCGR1A"  "CD68"    "S100A12"
#> 
#> $pos$`B cells`
#> [1] "CD19"  "MS4A1" "CD79A"
#> 
#> $pos$`T cells`
#> [1] "CD3D" "CD3E" "CD3G"
#> 
#> $pos$`CD4 T cells`
#> [1] "CD4"   "FOXP3" "IL2RA" "IL7R" 
#> 
#> $pos$`CD8 T cells`
#> [1] "CD8A" "CD8B"
#> 
#> $pos$`Dendritic cells`
#> [1] "\tIL3RA" "CD1C"    "BATF3"   "THBD"    "CD209 " 
#> 
#> 
#> $neg
#> NULL
#>