testPIMcontrast: Test contrast from PIMSeq results

In CenterForStatistics-UGent/PIMseq: PIM for testing differential expression in single cell RNA-seq data

Test contrast from PIMSeq results

Description

Tests contrasts using results obtained from PIMSeq function. This function can be called independently after fitting PIM for gene expression data.

Usage

testPIMcontrast(pim.res, contrasts, only.conditions = TRUE,
  gene.warning.return = FALSE, ...)

Arguments

pim.res	PIMSeq output
contrasts	a vector of coefficients for the linear combination of the factors
only.conditions	a logical value If only.conditions=TRUE (default), contrast will be tested among the coefficients of condition variables only. If only.conditions=FALSE, contrast will be tested considering all coefiecients in the model (conditions and nuisance variables). The dimension of the contrast matrix/vector depends on this argument.
gene.warning.return	a logical value to show warning message if the contrast test for a particular gene encounters an error. Default is FALSE.
...	additional arguiments

Value

a data frame containg the estimated linear factor, test statistic, standard error, p value, estimated PI, and FDR adjusted p value.

Examples

 # examples

CenterForStatistics-UGent/PIMseq documentation built on Jan. 15, 2024, 3:49 a.m.