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

Description Usage Arguments Details Value Author(s) See Also

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

1
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 Dec. 7, 2018, 8:02 a.m.