getTopMarkersByPropNew: Find specific marker gene for each cluster

In AllenInstitute/scrattch.hicat: Hierarchical Iterative Clustering Analysis for Transcriptomic data

Find specific marker gene for each cluster

Description

This function identifies the top marker gene (or "none") for each cluster based on the cluster medians and proportions of cells expressing a gene and based on various parameters.

Usage

getTopMarkersByPropNew(
  propExpr,
  medianExpr,
  propDiff = 0,
  propMin = 0.5,
  medianFC = 1,
  excludeGenes = NULL,
  sortByMedian = TRUE
)

Arguments

propExpr	matrix of proportions of cells expressing a gene in each cluster (genes=rows, clusters=columns)
medianExpr	matrix of median expression per cluster (genes=rows, clusters=columns)
propDiff	Must have difference in proportion higher than this value in "on" cluster compared with each other cluster
propMin	Must have higher proportion in "on" cluster
medianFC	Must have median fold change greater than this value in "on" group vs. each other cluster
excludeGenes	Genes exlcuded from marker consideration (NULL by default)
sortByMedian	Should genes passing all filters be prioritized by median fold change (TRUE, default) or by difference in proportion between clusters (FALSE)

Details

Note: this could potentially be replaced by an existing hicat function for identifying marker genes. This function is fast and chooses 'reasonable" genes.

Value

a vector of the top marker gene per cluster (or "none" for clusters with none)

AllenInstitute/scrattch.hicat documentation built on June 6, 2024, 5:31 a.m.