test.associated.genes: Determine a set of genes significantly associated with the...

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

Description

Determine a set of genes significantly associated with the tree

Usage

test.associated.genes(r, X, n.map = 1,
  n.cores = (parallel::detectCores()/2), spline.df = 3,
  fdr.cut = 1e-04, A.cut = 1, st.cut = 0.8, summary = FALSE,
  subtree = NA, fdr.method = NULL, ...)

Arguments

r	pptree object
X	expressinon matrix of genes (row) vs cells (column)
fdr.cut	FDR (Benjamini-Hochberg adjustment) cutoff on significance; significance if FDR < fdr.cut
A.cut	cmplitude cutoff on significance; significance if A > A.cut
st.cut	cutoff on stability (fraction of mappings with significant (fdr,A) pair) of association; significance, significance if A > A.cut
summary	show plot of amplitude vs FDR of each gene's association. By default FALSE.
subtree	restrict statistical assesment to a subtree
fdr.method	a method to adjust for multiple testing. Default - Bonferroni. Alternatively, "BH" can be used.

Value

modified pptree object with a new field r$stat.association that includes pvalue, amplitude, fdr, stability and siginificane (TRUE/FALSE) of gene associations

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