ChIPSeqSpikeDatasetList-class: ChIPSeqSpikeDatasetList Reference Class

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

Description

Class containing a list of ChIPSeqSpikeDataset objects

Fields

datasetList: A list of ChIPSeqSpikeDataset objects

Constructor

ChIPSeqSpikeDatasetList(dataset_list, verbose)

Arguments

dataset_list

A properly formatted list of information needed to create the object (see details).

verbose

Indicate if processing messages should be output.

Getters

getBigWigFile

Returns a vector of all bigWig paths corresponding to all files specified in info.csv

x[[i]]

Get the ChIPSeqSpikeDataset object at index i

Setters

x[[i]] <- value

Set value to ChIPSeqSpikeDatasetList i

Details

This class enables to process datasets containing different input files. It will creates a list of ChIPSeqSpikeDataset 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. spikeDataset function formats properly the different information into a dataset_list which is submitted to the ChIPSeqSpikeDatasetList constructor.

Author(s)

Nicolas Descostes

See Also

ChIPSeqSpikeDataset-class spikeDataset spikeSummary getRatio

Examples

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")

csds <- spikeDataset(infoFile = info_file_csv, bamPath = bam_path, 
                     bigWigPath = bigwig_path)

is(csds)
csds

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