expressionMatrixToDElist: Turn a Matrix of Gene Expression into a List of Differential...

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Turn a Matrix of Gene Expression into a List of Differential Expression Tables

Description

Transforms a matrix of gene expression values into a list of simple differential gene expression data frames. This is a reformatting utility for functions that operate on DE lists.

Usage

expressionMatrixToDElist(x, groups = colnames(x), minimumValue = NULL, AVG.FUN = mean)

Arguments

x	a numeric matrix of gene expression values, with rownames as the GeneIDs and column names for the SampleIDs
groups	a character vector of group identifiers of the same length as the column width of x
minimumValue	a small linear offset to add to all expression values, before taking the log2 of the ratios, to prevent divide by zero and compensate for very low expression values
AVG.FUN	the math function for averaging gene expression per group

Details

Many functions operate on DE lists, as generated by various differential expression tools that operate on transcriptome file sets. This utility function generates the same format, but starting from a matrix of gene expression values.

Value

A list of DE data frames, with a named element for each unique group in groups.

Author(s)

Bob Morrison

See Also

geneSetAnalysis for a typical example of a function that uses DE lists

robertdouglasmorrison/DuffyTools documentation built on April 16, 2024, 6:31 a.m.