filter_switchgenes: Extract switching gene list of interesting

In SGDDNB/GeneSwitches: Discover the order of gene regulatory events during cell state transitions

Description

This function extract a list of significant switching genes

Usage

filter_switchgenes(sce, allgenes = FALSE, pathway_name = NULL,
  genelists = GeneSwitches:::genelists,
  genetype = c("Surface proteins", "TFs"), zero_pct = 0.9,
  r2cutoff = 0.03, direction = c("up", "down"), topnum = 1e+05)

Arguments

sce	switching genes
allgenes	if use all genes
pathway_name	a list of pathway name(s) to plot
genelists	a gene list to plot
genetype	specific gene type to plot c("EMT", "reprogramming", "stem", "surface", "TF")
zero_pct	zero-expression percentage cut off for significant genes
r2cutoff	pseudo R^2 cutoff
direction	switching direction, up or down
topnum	number of top genes ordered by pseudo R^2 value

SGDDNB/GeneSwitches documentation built on Dec. 16, 2020, 9:32 a.m.