ArrayTV (version 1.10.0)

gcCorrectMain: gcCorrectMain

Description

Correct gc biases in array data. The user must provide a range of windows and this function will compute the tv score for each window and correct the arrays based upon the window with the highest tv score (i.e with window showing the most gc bias)

Usage

gcCorrectMain(Ms, chr, starts, samplechr, increms, maxwins, jittercorrection=FALSE, returnOnlyTV=FALSE, onlyGC=FALSE,providedGC=NULL,build, verbose=FALSE)

Arguments

Ms

A matrix holding the array values

chr

a vector indicating the chromosome of each probe (should be the same length as the number of rows in the array matrix)

starts

a vector holding the genomic coordinates of the start positions the probes (should be the same length as the number of rows inthe array matrix)

samplechr

a subset (or the entire set) of the chromosomes represented in the arrays. The probes on these chromosomes will be used to compute the tvScore

increms

a vector of integers

maxwins

a vector ofintegers with each value >= the corresponding value in increms. Corresponding values of maxwins and increms must have the same quotient. For instance, if increms is c(10,1000) then an acceptable value of maxwins would be(500,5000) because the quotients of the corresponding elements are both 5.

jittercorrection

if TRUE amplify the correction values by a small amount to decrease the autocorrelation of proximal probes

returnOnlyTV

if TRUE only return the tvScores rather than applying corrections

onlyGC

if TRUE return the gc fraction of each window (the result may be subsequently passed into the providedGC argument to be used in correction)

providedGC

a vector of gc values (fractions from zero to 1) to use for computing corrections. This should be the same length as the number of rows in the array, if provided

build

the build matching the array. This is used to load the BSgenome object. If the arrays are annotated based on hg18 this would be 'hg18', if the annotation is based on hg19 this would be 'hg19'.

verbose

provide output throughout computation

Value

The default is to return corrected values for the arrays passed in. This result will have the same dimensions as the first argument (the uncorrected values).if returnOnlyTV is TRUE this will be a matrix of tv score values, one row per window, one column per array. The rownames of the matrix will indicate the size of the window. If onlyGC=TRUE the gc fraction of each window will be returned.

Details

see example

References

Optimal window finding was inspired by a similar concept applied to gc correction for next generation sequencing experiments:Benjamini Y, Speed TP. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res 2012;40:e72

Examples

## Example with parallelization, setting the number of processors to 3

	path <- system.file("extdata", package="ArrayTV")
	load(file.path(path, "array_logratios.rda"))
	nimblegen[, "M"] <- nimblegen[, "M"]/1000

	increms <- c(10,1000,100e3)
	wins <- c(100,10e3,1e6)
        if(require(doParallel)){
	  ## nodes may be set to the number of cpus available
          nodes<-3
          cl <- makeCluster(nodes)
          registerDoParallel(cl)
        }

	## calculate tv scores in many windows and correct M values
	## using the best window
	nimcM1List <- gcCorrectMain(nimblegen[, "M", drop=FALSE],
				    chr=rep("chr15",nrow(nimblegen)),
				    starts=nimblegen[, "position"],
				    increms=increms,
				    maxwins=wins,
				    build='hg18')
	tvScores <- nimcM1List[['tvScore']]
	winsorted <- as.numeric(rownames(tvScores)[order(tvScores,decreasing=TRUE)])
	logwinsorted <- log(as.numeric(winsorted),10)
	logwinsortdiff <- abs(logwinsorted[1]-logwinsorted)
	## correct M values a 2nd time using a different window size
	nimcM2List <- gcCorrect(nimcM1List[['correctedVals']],
				chr=rep("chr15",nrow(nimblegen)),
				starts=nimblegen[, "position"],
				maxwins=winsorted[logwinsortdiff>=1][1],
				build='hg18')
        stopCluster(cl)
	## Refer to the vignette for details