Import the data from ChiP and input matrices

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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(DChIPRep)
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DChIPRep/importDataFromMatrices.Rd_%03d_medium.png", width=480, height=480)
> ### Name: importDataFromMatrices
> ### Title: Import the data from ChiP and input matrices
> ### Aliases: importDataFromMatrices
> 
> ### ** Examples
> 
> data(exampleSampleTable)
> data(exampleInputData)
> data(exampleChipData)
> imDataFromMatrices <- importDataFromMatrices(inputData = exampleInputData,
+ chipData = exampleChipData,
+ sampleTable = exampleSampleTable)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>