difftest: difftest
In TSCAN: Tools for Single-Cell Analysis

Description Usage Arguments Details Value Author(s) Examples

testing differentially expressed genes

1	difftest(data, TSCANorder, df = 3)

`data`	The raw single_cell data, which is a numeric matrix or data.frame. Rows represent genes/features and columns represent single cells.
`TSCANorder`	The TSCAN ordering generated by function `TSCANorder`.
`df`	Numeric value specifying the degree of freedom used in the GAM model.

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.

Data frame containing pvalues and qvalues of testing differentially expression.

Zhicheng Ji, Hongkai Ji <zji4@zji4.edu>

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