matBindingValues {ChIPSeqSpike} | R Documentation

## Set the matrices of binding values

### 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)
    }

[Package ChIPSeqSpike version 1.2.1 Index]