extract_genes_cell {scMappR}

Extract Markers

Description

Extracting cell-type markers from a signature matrix.

Usage

extract_genes_cell(
  geneHeat,
  cellTypes = "ALL",
  val = 1,
  isMax = FALSE,
  isPvalue = FALSE
)

Arguments

geneHeat

The heatmap of ranks from your scRNA-seq dataset with your genes subsetted.

cellTypes

The cell-types that you're interested in extracting. They need to be colnames (not case sensitive).

val

How associated a gene is with a particular cell type to include in your list - default is slightly associated.

isMax

If you are taking the single best CT marker (T/F) – TRUE not recommended.

isPvalue

If the signature matrix is raw p-value (T/F) – TRUE not recommended.

Details

This function takes a signature matrix and extracts cell-type markers above a p-value or fold-change threshold.

Value

extract_genes_cell A vector of genes above the threshold for each sample.

Examples

data(POA_example)
Signature <- POA_example$POA_Rank_signature
RowName <- get_gene_symbol(Signature)
rownames(Signature) <-RowName$rowname
# extract genes with a -log10(Padj > 1)
Signat <- extract_genes_cell(Signature)