id_markers: ID markers

In kgellatl/SignallingSingleCell: Network Analysis for single cell RNA sequencing Data (sc-RNASeq)

Description

This will perform marker gene identification

Usage

id_markers(input, id_by = "Cluster", print_progress = TRUE, overwrite = FALSE)

Arguments

input	the input ex_sc
id_by	a pData variable to run id_markers on. Defaults to "Cluster"
print_progress	will print progress if TRUE
overwrite	if TRUE will overwrite previously calculated scores on the same id_by variable

Details

This will find marker genes for each cluster. First, for each cluster it calculates the fraction of cells expressing a given gene, and the mean expression of that gene (within the cluster). It then compares these values to the values of all other groups looking for genes which maximize the distance in both fraction expressing and the mean expression.

Examples

ex_sc_example <- id_markers(input = ex_sc_example, print_progress = TRUE)

kgellatl/SignallingSingleCell documentation built on Dec. 29, 2021, 4:12 p.m.