DESeq.DiffExpress: Differential Expression by Group functions

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Differential Expression by Group functions

Description

Wrapper functions for calling various Differential Expression (DE) tools.

Usage

DESeq.DiffExpress( fnames, fids, m = NULL, groupSet, targetGroup = sort(groupSet)[1], 
		geneColumn = "GENE_ID", intensityColumn = "READS_M", keepIntergenics = FALSE, 
		minimumRPKM = 1, missingGenes = "fill", extraColumn = NULL, 
		average.FUN = sqrtmean, wt.folds = 1, wt.pvalues = 1, wt.dists = 1)

DESeq.DiffExpress( fnames, fids, m = NULL, groupSet, targetGroup = sort(groupSet)[1], 
		geneColumn = "GENE_ID", intensityColumn = "READS_M", keepIntergenics = FALSE, 
		minimumRPKM = 1, missingGenes = "fill", extraColumn = NULL, 
		average.FUN = sqrtmean, wt.folds = 1, wt.pvalues = 1, wt.dists = 1)

RankProduct.DiffExpress( fnames, fids, m = NULL, groupSet, targetGroup = sort(groupSet)[1], 
		geneColumn = "GENE_ID", intensityColumn = "READS_M", keepIntergenics = FALSE, 
		offset = 0, missingGenes = "fill", extraColumn = NULL, 
		average.FUN = sqrtmean, wt.folds = 1, wt.pvalues = 1, wt.dists = 1)

SAM.DiffExpress( fnames, fids, m = NULL, groupSet, targetGroup = sort(groupSet)[1], 
		geneColumn = "GENE_ID", intensityColumn = "READS_M", keepIntergenics = FALSE, 
		minimumIntensity = NULL, missingGenes = "fill", extraColumn = NULL, 
		average.FUN = sqrtmean, wt.folds = 1, wt.pvalues = 1, wt.dists = 1,
		needJitter = FALSE)

Arguments

fnames	a character vector of full pathnames to transcriptome files of gene expression
fids	a character vector of SampleIDs, one for each file
m	an optional matrix of gene expression, as an alternative to separate files for each sample. In this case, the GeneIDs are taken from the rownames of m and the SampleIDs are taken from the column names of m
groupSet	a character vector of group identifiers, one for each file, that categories that sample
targetGroup	a character string specifying the one group to be compared against all other groups
geneColumn	the name of the column in the transcriptome files that hold the GeneIDs
intensityColumn	the name of the column in the transcriptome files that hold the gene expression values
keepIntergenics	logical, should the named non-standard intergenic regions be kept in the final results
minimumRPKM, offset, minimumIntensity	linear offset added to all expression values, before taking log2 of the ratios, to prevent divide by zero and false fold change magnitudes from very low expression values
missingGenes	how to handle missing genes when combining all files of transcriptomes. See expressionFileSetToMatrix
extraColumn	a character vector of additional column names to be propegated from the transcriptome files to the resulting differential expression table
average.FUN	the math function for averaging gene expression values within each group
wt.folds, wt.pvalues, wt.dists	weighting terms for ordering the final results of differential expression. Passed to function diffExpressRankOrder
needJitter	SAM can break if there is no variance in a group of expression values, as may happen in some discrete data like proteome peptide abundance. This logical can force the expression to have some variance

Details

This family of functions dispatch various differential expression tools, all of which return a table of all genes, sorted into differential expression order such that genes most up-regulated in group targetGroup as compared to all other groups will be at the top, and most down-regulated genes at the bottom.

Value

a data frame of differential results, with a row for every gene in the transcriptomes, sorted into differential expression rank order. Column include:

comp1	Description of 'comp1'
comp2	Description of 'comp2'

Author(s)

Bob Morrison

See Also

metaRanks a low level tool for combining result files into a consensus ranking. metaResults a wrapper function for combining results from all 5 DE functons into a final consensus differential expression table.

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