pipe.ExtractPipelineSummaryDetails: Summarize Alignment Metrics

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

Summarize Alignment Metrics

Description

Tabulate the read counts and percentages for all alignment categories.

Usage

pipe.ExtractPipelineSummaryDetails(sampleIDset, optionsFile = "Options.txt", results.path = NULL, verbose = FALSE)
extractPipelineSummaryDetails(sampleIDset, optionsFile = "Options.txt", results.path = NULL, verbose = FALSE)

Arguments

sampleIDset	The set of SampleIDs to evaluate.
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'.

Details

Collects the read counts for all possible alignment outcomes, from raw input reads to NoHits, Ribo Cleared, Genomic, and Splices. Summarizes by both count and percentage.

When the samples are from a mixed species target, also gives a breakdown of aligned reads per species.

Reported counts are alway for unpaired reads, even if the data was processed as paired end data.

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (sampleIDset, optionsFile = "Options.txt", results.path = NULL, 
    verbose = FALSE) 
{
    ans <- extractPipelineSummaryDetails(sampleID = sampleIDset, 
        optionsFile = optionsFile, results.path = results.path, 
        verbose = verbose)
    write.table(ans, "Pipeline.SummaryDetails.csv", sep = ",", 
        quote = T, row.names = F)
    return(invisible(ans))
  }

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