R: Produce output data files, given annotation files and DEXSeq...

writeCompleteResults {JunctionSeq}

R Documentation

Produce output data files, given annotation files and DEXSeq exonCountSet object and DEXSeq results data.

Description

This function takes the raw DEXSeq results and merges in feature annotations, as well as calculating and merging in a number of different normalized and fitted values for each level of the condition variable.

Usage

writeCompleteResults(jscs, outfile.prefix, 
                        gzip.output = TRUE,
                        FDR.threshold = 0.01,
                        save.allGenes = TRUE, save.sigGenes = TRUE,
                        save.fit = FALSE, save.VST = FALSE,
                        save.bedTracks = TRUE,
                        save.jscs = FALSE,
                        bedtrack.format = c("BED", "GTF", "GFF3"),
                        verbose = TRUE)

Arguments

`jscs`	A `JunctionSeqCountSet`. Usually created by `runJunctionSeqAnalyses`. Alternatively, this can be created manually by `readJunctionSeqCounts`. However in this case a number of additional steps will be necessary: Dispersions and size factors must then be set, usually using functions `estimateSizeFactors` and `estimateJunctionSeqDispersions`. Hypothesis tests must be performed by `testForDiffUsage`. Effect sizes and parameter estimates must be created via `estimateEffectSizes`.
`outfile.prefix`	A string indicating the filename prefix where output files should be saved.
`gzip.output`	Logical. If `TRUE`, then all ".txt" text files should be gzip-compressed to save space.
`FDR.threshold`	The adjusted-p-value threshold used to determine statistical significance.
`save.allGenes`	Logical. Whether to save files containing data for all genes.
`save.sigGenes`	Logical. Whether to save a separate set of files containing data for only the significant genes. If this and save.allGenes are both true then two sets of files will be generated.
`save.fit`	Logical. Whether to save model fit data.
`save.VST`	Logical. Whether to save VST-transformed data.
`save.bedTracks`	Logical. Whether to save "bed" junction coverage tracks.
`save.jscs`	Logical. Whether to the entire `JunctionSeqCountSet` object. Default is FALSE.
`bedtrack.format`	Character string. The format to use for the browser tracks.
`verbose`	A boolean flag indicating whether or not to print progress information during execution. (Default=FALSE)

Details

Saves a wide variety of data from the analyses.

Value

This is a side-effecting function, and does not return a value.

Examples

data(exampleDataSet,package="JctSeqData");
#Write results tables and browser track files:
writeCompleteResults(jscs, outfile.prefix = "./results.");

## Not run: 
########################################
#Set up example data:
decoder.file <- system.file(
                  "extdata/annoFiles/decoder.bySample.txt",
                  package="JctSeqData");
decoder <- read.table(decoder.file,
                  header=TRUE,
                  stringsAsFactors=FALSE);
gff.file <- system.file(
            "extdata/cts/withNovel.forJunctionSeq.gff.gz",
            package="JctSeqData");
countFiles <- system.file(paste0("extdata/cts/",
     decoder$sample.ID,
     "/QC.spliceJunctionAndExonCounts.withNovel.forJunctionSeq.txt.gz"),
     package="JctSeqData");
######################
#Run example analysis:
jscs <- runJunctionSeqAnalyses(sample.files = countFiles,
           sample.names = decoder$sample.ID,
           condition=factor(decoder$group.ID),
           flat.gff.file = gff.file,
           analysis.type = "junctionsAndExons"
);
########################################

#Write results tables and browser track files:
writeCompleteResults(jscs, outfile.prefix = "./results.");


## End(Not run)

[Package JunctionSeq version 1.10.0 Index]