matBindingValues: Set the matrices of binding values

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

Description

Set a list of matrices of binding values that are used to plot boxplots and correlation plots.

Usage

matBindingValues(theObject) <- value
            
            
## S4 replacement method for signature 'ChIPSeqSpikeDataset'
matBindingValues(theObject) <- value

## S4 replacement method for signature 'ChIPSeqSpikeDatasetBoost'
matBindingValues(theObject) <- value

## S4 replacement method for signature 'ChIPSeqSpikeCore'
matBindingValues(theObject) <- value

Arguments

theObject	A ChIPSeqSpikeCore, ChIPSeqSpikeDataset or ChIPSeqSpikeDatasetBoost object
value	A list of matrices

Value

The modified object is returned

Author(s)

Nicolas Descostes

See Also

plotCor boxplotSpike

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 = FALSE, 
                      outputFolder = output_folder)

    new_list <- list(matrix(seq_len(10)), matrix(2:18))
    matBindingValues(csds[[1]]) <- new_list
    unlink("test_chipseqspike/", recursive = TRUE)
}

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