Read sgr data

Description

Function to read sgr files into a list object, quantile normalise signal.

Usage

readSgrFiles(X, dataPath = getwd(), fileExt=".txt", normalise = TRUE)

Arguments

Details

The function reads the data files in sgr file tab delimited format: chr, position, signal. All data sets must be from the same array platform and have the same chromosome names and positions. The data is read and then quantile normalised and stored as an ExpressionSet.

Value

Returns normalized, transformed values as an object of class ExpressionSet

Author(s)

Bettina Fischer

See Also

ExpressionSet

Examples

  sgrfiles <- c("SoxNDam_trunc","SoxN-DDam_trunc","DDam_trunc")
  dataPath <- system.file("extdata",package="SimBindProfiles")
  readTestSGR <- readSgrFiles(X=sgrfiles, dataPath)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(SimBindProfiles)
Loading required package: Ringo
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SimBindProfiles/readSgrFiles.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readSgrFiles
> ### Title: Read sgr data
> ### Aliases: readSgrFiles
> 
> ### ** Examples
> 
>   sgrfiles <- c("SoxNDam_trunc","SoxN-DDam_trunc","DDam_trunc")
>   dataPath <- system.file("extdata",package="SimBindProfiles")
>   readTestSGR <- readSgrFiles(X=sgrfiles, dataPath)
Reading /home/ddbj/local/lib64/R/library/SimBindProfiles/extdata/SoxNDam_trunc.txt ...
Reading /home/ddbj/local/lib64/R/library/SimBindProfiles/extdata/SoxN-DDam_trunc.txt ...
Reading /home/ddbj/local/lib64/R/library/SimBindProfiles/extdata/DDam_trunc.txt ...
Performing quantile normalisation...
Building ExpressionSet...

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>