difftest {TSCAN} | R Documentation

## difftest

### Description

testing differentially expressed genes

### Usage

    difftest(data, TSCANorder, 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.
`TSCANorder` | The TSCAN ordering generated by function `TSCANorder`.
`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 qvalues of testing differentially expression.

### Author(s)

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

### Examples

    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]

[Package TSCAN version 1.18.0 Index]