ComputeMarkers: Compute upregulated marker genes for each cell group in the...

In NHLBI-BCB/IKAP: IKAP: Identifying K mAjor cell Population group in single cell analysis

Description

This function computes the list of upregulated marker genes for each cell group in the Seurat object using Seurat::FindAllMarkers. It also computes the area under the ROC curve (AUROC) for each marker gene. Finally it saves all relevant in Excel sheets.

Usage

ComputeMarkers(sobj, gap.gain, candidates, out.dir)

Arguments

sobj	the Seurat object
gap.gain	a numeric matrix for the increase of gap statistic from k-1 to k. Columns are the number of clusters (k = 2 to k.max) and rows are the number of top principal components (nPC). For example, the first column is the increase of gap statistic from k=1 to k=2 for each nPC (row).
candidates	the list of candidates returned from SelectCandidate().
out.dir	the path for output directory

Examples

ComputeMarkers(sobj, gap.gain, candidates, out.dir)

NHLBI-BCB/IKAP documentation built on March 21, 2020, 8:08 p.m.