averageBindingValues: Set the binding values used to perform profiles and heatmaps

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

Description

Set a plotSetArray object to the plotSetArrayList slot of the given object.

Usage

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

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

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

Arguments

theObject	A ChIPSeqSpikeDataset, ChIPSeqSpikeDatasetBoost or ChIPSeqSpikeCore object
value	A PlotSetArray object

Value

The modified object is returned

Author(s)

Nicolas Descostes

See Also

plotProfile plotTransform plotHeatmaps PlotSetArray-class

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)
    test <- getAverageBindingValues(csds[[1]])
    averageBindingValues(csds[[1]]) <- test
}

unlink("test_chipseqspike/", recursive = TRUE)

descostesn/ChIPSeqSpike documentation built on Aug. 6, 2019, 3:51 p.m.