comppvalue: Computing P-values for Link Significance

In RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Computing P-values for Link Significance

Description

This function computes a p-value for the significance (i.e. over-representation of assigned cells) of each inter-cluster link.

Usage

comppvalue(object, pthr = 0.01, sensitive = FALSE)

Arguments

object	Ltree class object.
pthr	p-value cutoff for link significance. This threshold is applied for the calculation of link scores reflecting how uniformly a link is occupied by cells.
sensitive	logical. Only relevant when nmode=TRUE in function projcell. If TRUE, then all cells on the most highly significant link are and the link itself are disregard to test significance of the remaining links with a binomial p-value. Default is FALSE.

Value

An Ltree class object with link p-value and occupancy data stored in slot cdata.

Examples

sc <- SCseq(intestinalDataSmall)
sc <- filterdata(sc)
sc <- compdist(sc)
sc <- clustexp(sc)
sc <- findoutliers(sc)
sc <- comptsne(sc)
ltr <- Ltree(sc)
ltr <- compentropy(ltr)
ltr <- projcells(ltr)
ltr <- lineagegraph(ltr)
ltr <- comppvalue(ltr)

RaceID documentation built on April 4, 2025, 4:34 a.m.