exportBigWigs {ChIPSeqSpike} | R Documentation |
In boost mode, binding values of experiments are stored in the form of GRanges tables in the object. exportBigWigs output these values giving a proper bigwig file name corresponding to the transformations already performed.
exportBigWigs(theObject, verbose = TRUE) ## S4 method for signature 'ChIPSeqSpikeDatasetBoost' exportBigWigs(theObject, verbose = TRUE) ## S4 method for signature 'ChIPSeqSpikeDatasetListBoost' exportBigWigs(theObject, verbose = TRUE)
theObject |
|
verbose |
If FALSE, do not output processing messages. Default is TRUE |
Output bigwig files of binding values.
The suffix of the bigwig file reflects the transformation steps performed on the object. If all steps were performed, the file name will be of the form: 'expName-RPM-BGSub-reverse-spiked.bw'. The suffixes 'RPM', 'BGSub', 'reverse' and 'spiked' stands for RPM scaling, input subtraction, RPM scaling reversal and exogenous scaling respectively.
ChIPSeqSpikeDatasetBoost
: Method for signature theObject=
'ChIPSeqSpikeDatasetBoost'
ChIPSeqSpikeDatasetListBoost
: Method for signature theObject=
'ChIPSeqSpikeDatasetListBoost'
Nicolas Descostes
## Mock example on a restricted number of reads info_file_csv <- system.file("extdata/info.csv", package="ChIPSeqSpike") bam_path <- system.file(c("extdata/bam_files"), package="ChIPSeqSpike") bigwig_path <- system.file(c("extdata/bigwig_files"), package="ChIPSeqSpike") if(.Platform$OS.type != 'windows') { csds <- spikeDataset(infoFile = info_file_csv, bamPath = bam_path, bigWigPath = bigwig_path, boost = TRUE) ## Creating test folder dir.create("./test_chipseqspike") csds <- estimateScalingFactors(csds) ## Apply RPM scaling csds <- scaling(csds, outputFolder = "test_chipseqspike") ## output RPM scaled files exportBigWigs(csds) ## Apply input subtraction csds <- inputSubtraction(csds) ## output input subtracted files exportBigWigs(csds) ## Delete all files generated in this example unlink("test_chipseqspike/", recursive = TRUE) }