ChIPSeqSpikeDatasetListBoost-class: ChIPSeqSpikeDatasetListBoost Reference Class
In ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

Description Fields Constructor Arguments Getters Details Author(s) See Also Examples

Class containing a list of ChIPSeqSpikeDatasetBoost objects

datasetList: A list of ChIPSeqSpikeDatasetBoost objects

ChIPSeqSpikeDatasetListBoost(dataset_list, verbose)

dataset_list: A properly formatted list of information needed to create the object (see details).
verbose: Indicate if processing messages should be output.

exportBigWigs: Output all bigwig files corresponding to the previously performed transformations. The list of bigwig files is given in info.csv (see details).
x[[i]]: Get the ChIPSeqSpikeDatasetBoost object at index i

This class enables to process datasets containing different input files in boost mode. It will creates a list of ChIPSeqSpikeDatasetBoost objects, each of them containing a different input.

The above indicated constructor should not be used directly. One would rather create the object by calling the "meta-constructor" spikeDataset function, which takes a info.csv file as input, setting boost = TRUE. spikeDataset function formats properly the different information into a dataset_list which is submitted to the ChIPSeqSpikeDatasetListBoost constructor.

Nicolas Descostes

ChIPSeqSpikeDatasetBoost-class spikeDataset spikeSummary getRatio

info_file_csv <- system.file("extdata/info.csv", package="ChIPSeqSpike")
bam_path <- system.file(c("extdata/bam_files"), package="ChIPSeqSpike")
bigwig_path <- system.file(c("extdata/bigwig_files"), package="ChIPSeqSpike")

if(.Platform$OS.type != 'windows') {
    csds <- spikeDataset(infoFile = info_file_csv, bamPath = bam_path, 
                         bigWigPath = bigwig_path, boost = TRUE)
    is(csds)
    csds
}