importDataFromMatrices: Import the data from ChiP and input matrices

In DChIPRep: DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication

Description

This function imports the data from two matrices that contain counts summarized per position. It computes the normalization factors from the input (one per position) and creates a DChIPRepResults object.

Usage

importDataFromMatrices(inputData, chipData, sampleTable)

Arguments

inputData	a matrix containing the counts for the input per position.
chipData	a matrix containing the counts for the ChIP per position.
sampleTable	a data.frame that has to contain the columns sampleID, upstream, downstream and condition. Each row of the table describes one experimental sample. See data(exampleSampleTable) for an example table. and the vignette for further information.

Details

The normalization factors are computed as t(t(inputData) * (covC/covI)) , Where covC and covI contain the total sum of the ChIP and the input samples. Zero normalization factors can arise if the input has zero counts for certain positions. That's why input values equal to zero are set to 1 in order to always obtain valid normalizationFactors.

Value

a DChIPRepResults object containing the imported data as a DESeqDataSet.

Examples

data(exampleSampleTable)
data(exampleInputData)
data(exampleChipData)
imDataFromMatrices <- importDataFromMatrices(inputData = exampleInputData,
chipData = exampleChipData,
sampleTable = exampleSampleTable)

DChIPRep documentation built on April 29, 2020, 4:26 a.m.