bigWigFile: Set the path to the bigwig file

In ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

Description

Set the path to the input or experiment bigwig file.

Usage

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

Arguments

theObject	A ChIPSeqSpikeCore, ChIPSeqSpikeDataset, ChIPSeqSpikeDatasetBoost, Experiment or ExperimentLoaded object
value	A string representing a path to a bigwig file

Details

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.

Value

The modified object is returned

Author(s)

Nicolas Descostes

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")

## 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)

ChIPSeqSpike documentation built on Nov. 8, 2020, 5:29 p.m.