branch.specific.genes: Assign genes differentially expressed between two...

In hms-dbmi/crestree: Analysis of branching branching trajectories from single-cell data

Description

Assign genes differentially expressed between two post-bifurcation branches

Usage

branch.specific.genes(fork.de, stf.cut = 0.7, effect.b1 = 0.1,
  effect.b2 = 0.3, pd.a = 0, pd.p = 0.05)

Arguments

fork.de	statistics on expression differences betwee post-bifurcation branches, return of test.fork.genes
stf.cut	fraction of projections when gene passed fdr < 0.05
effect.b1	expression differences to call gene as differentially upregulated at branch 1
effect.b2	expression differences to call gene as differentially upregulated at branch 2
pd.a	minium expression increase at derivative compared to progenitor branches to call gene as branch-specific
pd.p	p-value of expression changes of derivative compared to progenitor branches to call gene as branch-specific

Value

table fork.de with added column stat, which classfies genes in branch-specifc (1 or 2) and non-branch-specific (0)

hms-dbmi/crestree documentation built on July 11, 2019, 8:04 p.m.