pipe.RIPpeaksToAltGeneMap: Combine RIP Peaks into an Alternate Gene Map

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

Combine RIP Peaks into an Alternate Gene Map

Description

Merge RIP peaks from multiple samples into one set of gene-like features that can be quantified for abundance and differential expression.

Usage

pipe.RIPpeaksToAltGeneMap(sampleIDset, annotationFile = "Annotation.txt", 
		optionsFile = "Options.txt", speciesID = NULL, results.path = NULL, 
		max.pvalue = 0.05)

Arguments

sampleIDset	Vector of SampleIDs for merging RIP peak data.
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.
speciesID	The SpeciesID of the target species to calculate a transcriptome for. By default, transcriptome for all species in the current target are generated.
results.path	The top level folder path for writing result files to. By default, read from the Options file entry 'results.path'.
max.pvalue	The limiting P-value for determining which peaks from each sample to include in the final set of peaks.

Details

This is second pipeline step for doing RIP peak analyses. Given a set of samples each with their own files of RIP peak results already generated, this function combines them all into one merged set of RIP peaks. And then returns those final peaks in a "Gene Map" format that is directly usable by all the transcriptome and differential expression pipes.

Peaks from different samples that overlap on the same strand are merged such the the final peak encloses all original smaller peaks. A peak need only occur in any one sample for it to be represented in the final set. In this way, any RIP peak feature that was detected in any sample will be a location that gets quantified and compared across sample groups in the downstream analyses.

Value

A data frame of RIP peak locations, in the format of a Gene Map, directly usable by downstream tools like pipe.Transcriptome and pipe.DiffExpression and pipe.MetaResults. Columns include:

GENE_ID	the unique identifier for this RIP peak. It combines the most proximal GeneID with the center point of this RIP peak
POSITION	the starting edge of the RIP peak region to be evaluated
END	the stopping edge of the RIP peak region to be evaluated
SEQ_ID	the chromosome name where this peak is located
STRAND	which chromosome strand the peak was found on. Note that RIP peaks are always strand specific, so there may be 2 separate peaks covering the same genomic location
NAME	the name of the most proximal GeneID
PRODUCT	the gene product term from the most proximal GeneID
N_EXON_BASES	the size of the peak in nucleotides
also	other columns that identify which one sample this RIP peak was most detected in, with all the peak scoring details from that sample's RIP peak results. Intended just for information purposes to tie final peaks back to their source sample, not used by any downstream tools

Author(s)

Bob Morrison

See Also

pipe.RIPpeaks to call RIP peaks for a single sample. MapSets for background on Gene Maps.

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