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Last data update: 2014.03.03

R: Import the data after running the Python script

importData

R Documentation

Import the data after running the Python script

Description

This function imports the data from the count table files as returned by the accompanying Python script.

Usage

importData(sampleTable, directory = "", ID = "name", ...)

Arguments

`sampleTable`	a data.frame that has to contain the columns ChiP, Input, sampleID, upstream, downstream and condition. Each row of the table describes one experimental sample. Each row of the table describes one experimental sample. See `data(exampleSampleTable)` for an example table. and the vignette for further information.
`directory`	the directory relative to which the filenames are specified given as a character.
`ID`	character giving the name of the feature identifier column in the count tables. Defaults to `"name"`
`...`	parameters passed to `summarizeCountsPerPosition`

Value

a DChIPRepResults object containg the imported data as a DESeqDataSet.

Examples

data(exampleSampleTable)
directory <- file.path(system.file("extdata", package="DChIPRep"))
importedData <- importData(exampleSampleTable, directory)

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.
You are welcome to redistribute it under certain conditions.
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/importData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: importData
> ### Title: Import the data after running the Python script
> ### Aliases: importData
> 
> ### ** Examples
> 
> data(exampleSampleTable)
> directory <- file.path(system.file("extdata", package="DChIPRep"))
> importedData <- importData(exampleSampleTable, directory)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>