count {ChIPSeqSpike} | R Documentation |
Set the number of endogenous reads associated to an experiment. This is used to compute scaling factors.
count(theObject) <- value ## S4 replacement method for signature 'ChIPSeqSpikeDataset' count(theObject) <- value ## S4 replacement method for signature 'ChIPSeqSpikeDatasetBoost' count(theObject) <- value ## S4 replacement method for signature 'Experiment' count(theObject) <- value ## S4 replacement method for signature 'ExperimentLoaded' count(theObject) <- value ## S4 replacement method for signature 'ChIPSeqSpikeCore' count(theObject) <- value
theObject |
A |
value |
A numeric representing the number of mapped reads |
If the object is ChIPSeqSpikeCore, ChIPSeqSpikeDataset or ChIPSeqSpikeDatasetBoost, count will set the number of input DNA mapped reads to the endogenous reference genome.
If the object is Experiment or ExperimentLoaded, count will set the number of experiment mapped reads to the endogenous reference genome.
The modified object is returned
Nicolas Descostes
exoCount
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) getCount(csds[[1]][[1]]) count(csds[[1]][[1]]) <- 10 getCount(csds[[1]][[1]]) unlink("test_chipseqspike/", recursive = TRUE) }