bigWigFile {ChIPSeqSpike} | R Documentation |
Set the path to the input or experiment bigwig file.
bigWigFile(theObject) <- value ## S4 replacement method for signature 'ChIPSeqSpikeDataset' bigWigFile(theObject) <- value ## S4 replacement method for signature 'ChIPSeqSpikeDatasetBoost' bigWigFile(theObject) <- value ## S4 replacement method for signature 'Experiment' bigWigFile(theObject) <- value ## S4 replacement method for signature 'ExperimentLoaded' bigWigFile(theObject) <- value ## S4 replacement method for signature 'ChIPSeqSpikeCore' bigWigFile(theObject) <- value
theObject |
A |
value |
A string representing a path to a bigwig file |
If the object is ChIPSeqSpikeCore, ChIPSeqSpikeDataset or ChIPSeqSpikeDatasetBoost, bigWigFile will set the path to the input DNA experiment bigwig file corresponding to all experiments defined by the object.
If the object is Experiment or ExperimentLoaded, bigWigFile will set the path to the experiment bigwig file.
The modified object is returned
Nicolas Descostes
info_file_csv <- system.file("extdata/info.csv", package="ChIPSeqSpike") bam_path <- system.file("extdata/bam_files", package="ChIPSeqSpike") bigwig_path <- system.file("extdata/bigwig_files", package="ChIPSeqSpike") gff_vec <- system.file("extdata/test_coord.gff", package="ChIPSeqSpike") genome_name <- "hg19" output_folder <- "test_chipseqspike" bigwig_files <- system.file("extdata/bigwig_files", c("H3K79me2_0-filtered.bw", "H3K79me2_100-filtered.bw", "H3K79me2_50-filtered.bw", "input_0-filtered.bw", "input_100-filtered.bw", "input_50-filtered.bw"), package="ChIPSeqSpike") ## Copying example files dir.create("./test_chipseqspike") result <- file.copy(bigwig_files, "test_chipseqspike") if(.Platform$OS.type != 'windows') { csds <- spikePipe(info_file_csv, bam_path, bigwig_path, gff_vec, genome_name, verbose = TRUE, outputFolder = output_folder) write("toto", file="./test_chipseqspike/toto.bw") getBigWigFile(csds[[1]][[1]]) bigWigFile(csds[[1]][[1]]) <- "test_chipseqspike/toto.bw" getBigWigFile(csds[[1]][[1]]) } unlink("test_chipseqspike/", recursive = TRUE)