CNEr (version 1.8.3)

blatCNE: Wrapper function of blat for CNEs

Description

This wrapper function blat the CNEs against the reference genome.

Usage

blatCNE(CNE, winSize, cutoffs1, cutoffs2, assembly1Twobit, assembly2Twobit, blatOptions=NULL, cutIdentity=90, tmpDir=tempdir(), blatBinary="blat")

Arguments

CNE

A object of data.frame. Usually it is generated from cneMerge function.

winSize

A object of integer. The window size used for identifying the CNEs, such as 50 or 30.

cutoffs1, cutoffs2

A object of integer. The CNEs with more than the cutoff hits on the reference genome are removed.

assembly1Twobit, assembly2Twobit

A object of character. The path of reference genome in two bit file format.

blatOptions

A object of character. When it is NULL, a bunch of preset parameters for blat will be given based on the winSize parameter.

cutIdentity

A object of integer. Sets minimum sequence identity (in percent) in blat. Default is 90.

tmpDir

A object of character. By default, the R's temp dir is used. You can specify other path if your R's temp dir is small.

blatBinary

A object of character. The path of blat binary.

Value

A data.frame containing the CNEs is returned.

Details

When winSize > 45, the blat options is "-tileSize=11 -minScore=30 -repMatch=1024". When 35 < winSize

Examples

  ## Not run: 
#     assemblyHg19Twobit = "/Users/gtan/CSC/CNEr/2bit/hg19.2bit"
#     assemblyDanRer7Twobit = "/Users/gtan/CSC/CNEr/2bit/danRer7.2bit"
#     cneBlatedDanRer7Hg19 = list()
#     for(i in 1:length(cneMergedDanRer7Hg19)){
#       cneBlatedDanRer7Hg19[[names(cneMergedDanRer7Hg19)[i]]] = 
#       blatCNE(cneMergedDanRer7Hg19[[i]], 
#         as.integer(sub("\d+_", "", names(cneMergedDanRer7Hg19)[i])), 
#         cutoffs1=4L, cutoffs2=8L, 
#         assembly1Twobit=assemblyDanRer7Twobit, 
#         assembly2Twobit=assemblyHg19Twobit,
#         blatBinary="blat")
#       }
#     ## End(Not run)