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

In jtcasemajor/GENEXPRESSO: Comparison of DEG and coexpression tools

Description

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

Usage

tools.DEG.Microarrays.merge(data, tools, n1, n2)

Arguments

data	Dataframe with genes in row, and methods used in columns. It contains the differentially expressed p-values for each gene.
tools	Different methods are used to compute pvalues of differentially expressed genes for microarrays "Wilcox" uses the wilcoxDEG() function implemented in this very same package "limma" and "GEOlimma uses respectively the functions DEG_limma() and DEG_GEOlimma() that come from the limma package "RankProduct","RankProduct.log" perform a Rank Product analysis with the RankProducts() function from the RankProd package for normal and logged values respectively "RankSum","RankSum.log" perform a Rank Sum analysis with the RankProducts() function from the RankProd package for normal and logged values respectively
n1	Number of samples for the first experimental condition
n2	Number of samples for the second experimental condition

Value

Dataframe of pvalues of genes being differentially expressed with genes in columns and methods 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 Pvalues for all the methods 
tools = c("limma", "Wilcox","RankProduct","RankProduct.log","RankSum","RankSum.log")
res.DEG = tools.DEG.Microarrays.merge(Data,tools,10,10)

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