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 1.16.0 Index]