DEG_alternative: Takes the results of DEG_GEOlimma and DEG_limma and extracts...

In jtcasemajor/GENEXPRESSO: Comparison of DEG and coexpression tools

Description

Takes the results of DEG_GEOlimma and DEG_limma and extracts the pvalues of alternative hypothesis.

Usage

DEG_alternative(res.diff_limma)

Arguments

res.diff_limma

A dataframe with 3 columns is returned. It contains the Log Fold change value (logFC), The Pvalue associated with this Pvalue (PValue), the last column corresponds to the gene names (SYMBOL).

Value

A dataframe with 3 columns is returned. The two columns corresponds to the pvalue of a gene being more expressed and less expressed, in the second condition

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 

#Build the design matrix
#design = make_designMatrix(dataset = Data,ncond1 = 10, ncond2 = 10)
#get the results of limma analysis
#res.diff = DEG_limma(dataset = Data,design)

#compute the results of alternative hypothesis
#res.diff.alternative = DEG_alternative(res.diff)

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