deGene: Analysis of gene differential expression.

In Linlab-slu/TSSr: TSS sequencing data analysis

Analysis of gene differential expression.

Description

Analyzes gene-level differential expression using DESeq2 method (Love et al., 2014).

Usage

deGene(object,comparePairs=list(c("control","treat")), pval = 0.01,
 useMultiCore=FALSE, numCores = NULL)

## S4 method for signature 'TSSr'
deGene(
  object,
  comparePairs = list(c("control", "treat")),
  pval = 0.01,
  useMultiCore = FALSE,
  numCores = NULL
)

Arguments

object	A TSSr object.
comparePairs	Specified list of sample pairs for comparison with DESeq2 method.
pval	Genes with adjusted p value >= pVal will be returned. Default value = 0.01.
useMultiCore	Logical indicating whether multiple cores are used (TRUE) or not (FALSE). Default is FALSE.
numCores	Number of cores are used in clustering step. Used only if useMultiCore = TRUE. Default is NULL.

Value

Large List of elements - one element for each sample

Examples

data(exampleTSSr)
deGene(exampleTSSr,comparePairs=list(c("control","treat")), pval = 0.01)

Linlab-slu/TSSr documentation built on Oct. 23, 2024, 8:31 p.m.