tools.DEG.RNAseq.merge: Merge the DEG Pvalues for each tool used by tools.DEG.RNAseq...
In jtcasemajor/CPRD: Comparison of DEG and coexpression tools

Description Usage Arguments Value Examples

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

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

`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"

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

# 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)