deGene: Analysis of gene differential expression.

Description Usage Arguments Examples

Description

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

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
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.

Examples

1
deGene(exampleTSSr,comparePairs=list(c("control","treat")), pval = 0.01)

Linlab-slu/TSSr documentation built on July 28, 2021, 12:59 a.m.