writeCompleteResults {JunctionSeq} | R Documentation |
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.
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)
jscs |
A Alternatively, this can be created manually by |
outfile.prefix |
A string indicating the filename prefix where output files should be saved. |
gzip.output |
Logical. If |
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 |
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) |
Saves a wide variety of data from the analyses.
This is a side-effecting function, and does not return a value.
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)