count {ChIPSeqSpike}R Documentation

Set the number of reads associated to an experiment

Description

Set the number of endogenous reads associated to an experiment. This is used to compute scaling factors.

Usage

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

Arguments

theObject

A ChIPSeqSpikeDataset, ChIPSeqSpikeDatasetBoost, Experiment, ExperimentLoaded or ChIPSeqSpikeCore object

value

A numeric representing the number of mapped reads

Details

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.

Value

The modified object is returned

Author(s)

Nicolas Descostes

See Also

exoCount estimateScalingFactors

Examples

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)
}

[Package ChIPSeqSpike version 1.12.0 Index]