Assignment of cells to phenotypes based on selected markers

Source: R/GEX_phenotype.R

Adds a column to a VGM[[2]] Seurat object containing cell phenotype assignments. Defaults for T and B cells are available. Marker sets are customizable as below

GEX_phenotype(seurat.object, cell.state.names, cell.state.markers, default)

Arguments

seurat.object

A single seurat object / VDJ_GEX_matrix.output[[2]] object

cell.state.names

Character vector containing the cell state labels defined by the markers in cell.state.markers parameter. Example is c("NaiveCd4","MemoryCd4").

cell.state.markers

Character vector containing the gene names for each state. ; is used to use multiple markers within a single gene state. Different vector elements correspond to different states. Order must match cell.state.names containing the c("CD4+;CD44-","CD4+;IL7R+;CD44+").

default

Default is TRUE - will use predefined gene sets and cell states.

Value

Returns the input Seurat object with an additional column

Examples

vgm.phenotyped <- GEX_phenotype(seurat.object = Platypus::small_vgm[[2]]
, default = TRUE)