difftest {TSCAN} | R Documentation |
testing differentially expressed genes
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 |
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]