exogenousScalingFactor {ChIPSeqSpike} | R Documentation |
Set the exogenous scaling factor associated to an experiment
exogenousScalingFactor(theObject) <- value ## S4 replacement method for signature 'Experiment' exogenousScalingFactor(theObject) <- value ## S4 replacement method for signature 'ExperimentLoaded' exogenousScalingFactor(theObject) <- value
theObject |
An |
value |
A numeric representing the exogenous scaling factor |
A scaling factor is defined as:
1/(bam_count/1000000)
The modified object is returned
Nicolas Descostes
scalingFactor
estimateScalingFactors
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") if(.Platform$OS.type != 'windows') { ## Copying example files dir.create("./test_chipseqspike") result <- file.copy(bigwig_files, "test_chipseqspike") csds <- spikePipe(info_file_csv, bam_path, bigwig_path, gff_vec, genome_name, verbose = TRUE, outputFolder = output_folder) getExogenousScalingFactor(csds[[1]][[1]]) exogenousScalingFactor(csds[[1]][[1]]) <- 5 getExogenousScalingFactor(csds[[1]][[1]]) unlink("test_chipseqspike/", recursive = TRUE) }