difftest: difftest

In zji90/TSCAN: TSCAN: Tools for Single-Cell ANalysis

difftest

Description

testing differentially expressed genes

Usage

difftest(data, order, df = 3)

Arguments

data	The raw single_cell data, which is a numeric matrix or data.frame. Rows represent genes/features and columns represent single cells.
order	A character vector of pseudotime cell ordering. Must be within the column names of data.
df	Numeric value specifying the degree of freedom used in the GAM model.

Details

This function tests whether a gene is significantly expressed given pseudotime ordering. Likelihood ratio test is performed to compare a generalized additive model (GAM) with a constant fit to get the p-values. The p-values are adjusted for multiple testing by fdr.

Value

Data frame containing pvalues and FDRs of testing differential expression.

Author(s)

Zhicheng Ji, Hongkai Ji <[e-mail]>

Examples

data(lpsdata)
procdata <- preprocess(lpsdata)
lpsorder <- TSCANorder(exprmclust(procdata),orderonly=TRUE)
diffval <- difftest(procdata[1:10,],lpsorder)
#Selected differentially expressed genes under qvlue cutoff of 0.05
row.names(diffval)[diffval$qval < 0.05]

zji90/TSCAN documentation built on Sept. 14, 2022, 10:56 a.m.