Count probe GC content

Description

Return the GC content for each probe

Usage

countGC(dat, type = "pm", idx)

Arguments

Details

This function returns the sum of #G + #C in the pm or bg probes.

Value

a numeric vector

Author(s)

Martin Aryee <aryee@jhu.edu>

See Also

readCharm

Examples

	if (require(charmData)) {
		phenodataDir <- system.file("extdata", package="charmData")
		pd <- read.delim(file.path(phenodataDir, "phenodata.txt"))
		pd <- subset(pd, sampleID=="441_liver")
		dataDir <- system.file("data", package="charmData")
		setwd(dataDir)
		rawData <- readCharm(files=pd$filename, sampleKey=pd)
		ngc <- countGC(rawData)
		head(ngc)
	}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(charm)
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: SQN
Loading required package: mclust
Package 'mclust' version 5.2
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: nor1mix
Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.3-0 (2015-10-24) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    backsolve, forwardsolve

Loading required package: maps

 # maps v3.1: updated 'world': all lakes moved to separate new #
 # 'lakes' database. Type '?world' or 'news(package="maps")'.  #



Attaching package: 'maps'

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

    map

Loading required package: RColorBrewer
Loading required package: genefilter
Welcome to charm version 2.18.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/charm/countGC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: countGC
> ### Title: Count probe GC content
> ### Aliases: countGC
> 
> ### ** Examples
> 
> 	if (require(charmData)) {
+ 		phenodataDir <- system.file("extdata", package="charmData")
+ 		pd <- read.delim(file.path(phenodataDir, "phenodata.txt"))
+ 		pd <- subset(pd, sampleID=="441_liver")
+ 		dataDir <- system.file("data", package="charmData")
+ 		setwd(dataDir)
+ 		rawData <- readCharm(files=pd$filename, sampleKey=pd)
+ 		ngc <- countGC(rawData)
+ 		head(ngc)
+ 	}
Loading required package: charmData
Loading required package: pd.charm.hg18.example
Loading required package: RSQLite
Loading required package: DBI
Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
Loading required package: oligo
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'stats4'

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

    mle


Attaching package: 'S4Vectors'

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

    colMeans, colSums, rowMeans, rowSums

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
================================================================================
Welcome to oligo version 1.36.1
================================================================================
The following columns in sampleKey contain discrepant values between channels and are being removed: 1
Platform design info loaded.
Checking designs for each XYS file... Done.
Allocating memory... Done.
Reading ./136421_532.xys.
Checking designs for each XYS file... Done.
Allocating memory... Done.
Reading ./136421_635.xys.
[1] 23 33 37 37 34 25
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> dev.off()
null device 
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