tools.DEG.RNAseq.merge: Merge the DEG Pvalues for each tool used by tools.DEG.RNAseq...

In jtcasemajor/GENEXPRESSO: Comparison of DEG and coexpression tools

Description

Merge the DEG Pvalues for each tool used by tools.DEG.RNAseq in one dataframe

Usage

tools.DEG.RNAseq.merge(data, tools)

Arguments

data	Dataframe with genes in row, and methods used in columns. In contains the differentially expressed p-values for each gene.
tools	list character string. By default all the methods present in tools.DEG.RNAseq() are used. Any tools given in this list could be passed as argument : "edgeR_RLE","edgeR_upperquartile","edgeR_TMMwsp","deseq2.Wald","deseq2.LRT", "deseq"

Value

Dataframe of DEG pvalues with genes in columns and tools in rows.

Examples

# Import the dataset
Data = matrix(runif(5000, 10, 100), ncol=20)
group = paste0(rep(c("control", "case"), each = 10),rep(c(1:10),each = 1))
genes <- paste0(rep(LETTERS[1:25], each=10), rep(c(1:10),each = 1))
colnames(Data) = group
row.names(Data) = genes 

# Compute all the possible pvalues
# res.DEG = tools.DEG.RNAseq.merge(Data)

# Compute the pvalues, only with edgeR methods
tools = c("edgeR_RLE","edgeR_upperquartile","edgeR_TMM")
res.DEG = tools.DEG.RNAseq.merge(data = Data, tools = tools)

jtcasemajor/GENEXPRESSO documentation built on Dec. 21, 2021, 4:11 a.m.