pipe.DiffExpression: Turn Pairs of Transcriptomes into Differential Gene...

In robertdouglasmorrison/DuffyNGS: Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq

Turn Pairs of Transcriptomes into Differential Gene Expression Ratio Files

Description

This pipe takes transcriptome files as input, and creates ratio files that measure the differential gene expression as both fold change and P-values. Ratio files are then used as input to the Round Robin differential expression pipe.

Usage

pipe.DiffExpression(sampleIDset, groupSet = NULL, annotationFile = "Annotation.txt", 
		optionsFile = "Options.txt", results.path = NULL, speciesID = NULL, 
		altGeneMap = NULL, altGeneMapLabel = NULL, minRPKM = NULL, 
		missingOnly = FALSE, verbose = TRUE)

Arguments

sampleIDset	Vector of SampleIDs, giving the set of transcriptome samples to use for making ratio files.
groupSet	Vector of grouping labels, the same length as sampleIDset, giving the group membership for each sample. Only pairs of samples from different groups are turned into ratio files. Pairs of samples from the same group are silently ignored.
annotationFile	File of sample annotation details, which specifies all needed sample-specific information about the samples under study. See DuffyNGS_Annotation.
optionsFile	File of processing options, which specifies all processing parameters that are not sample specific. See DuffyNGS_Options.
results.path	The top level folder path for writing result files to. By default, read from the Options file entry 'results.path'.
speciesID	The SpeciesID of the target species to calculate ratio files for. By default, transcriptomes from all species in the current target are used to generate ratio files for all species.
altGeneMap	An alternate data frame of gene annotations, in a format identical to getCurrentGeneMap, that has the gene names and locations to be measured for read pileup depth. By default, use the standard built-in gene map for each species.
altGeneMapLabel	A character string identifier for the alternate gene map, that becomes part of all created path and file names to indicate the gene map that produced those transcriptomes.
minRPKM	Numeric offset that is added to all gene expression values before calculating the fold change ratio, to prevent division by zero and extremely high ratios from extremely low expression values. By default, takes its value from the DE.minimumRPKM option. Note the option can use a species specific suffix to allow automatic use of different minimums for different species in a mixed organism experiment.
missingOnly	Logical, controls whether all ratio files are re-calculated, or if only those that are not yet found in the ratios folder get created.

Details

This pipe is perhaps slightly misnamed, in that it only does many simple 2-sample comparisons, to create the ratio files needed by the Round Robin pipe, the oldest and originally only DE tool in the DuffyNGS suite. True group-wise differential expression pipes are mentioned below.

Value

A family of files is created in the ratio subfolder, containing the 2-way fold change differential expression comparison between transcriptomes from 2 different group categories.

Author(s)

Bob Morrison

See Also

pipe.DESeq pipe.EdgeR pipe.RankProduct pipe.RoundRobin pipe.SAM for the 5 separate Differential Expression tools that do group versus group comparisons.

pipe.MetaResults for the dispatching and final merging & averaging of all 5 DE tools.

robertdouglasmorrison/DuffyNGS documentation built on March 24, 2024, 4:16 p.m.