### R code from vignette source 'package_vignettes.Snw' ################################################### ### code chunk number 1: package_vignettes.Snw:31-33 (eval = FALSE) ################################################### ## library(GOTHiC) ## data(lymphoid_chr20_paired_filtered) ################################################### ### code chunk number 2: package_vignettes.Snw:79-84 (eval = FALSE) ################################################### ## dirPath = system.file("extdata", package="HiCDataLymphoblast") ## fileName1 = list.files(dirPath, full.names=TRUE)[1] ## fileName2 = list.files(dirPath, full.names=TRUE)[2] ## paired = pairReads(fileName1, fileName2, sampleName="lymphoid_chr20", ## DUPLICATETHRESHOLD = 1, fileType="Table") ################################################### ### code chunk number 3: package_vignettes.Snw:91-96 (eval = FALSE) ################################################### ## data(lymphoid_chr20_paired_filtered) ## mapped=mapReadsToRestrictionSites(filtered, sampleName="lymphoid_chr20", ## BSgenomeName="BSgenome.Hsapiens.UCSC.hg18", ## genome=BSgenome.Hsapiens.UCSC.hg18, ## restrictionSite="A^AGCTT", enzyme="HindIII", parallel=FALSE, cores=1) ################################################### ### code chunk number 4: package_vignettes.Snw:103-111 (eval = FALSE) ################################################### ## dirPath = system.file("extdata", package="HiCDataLymphoblast") ## fileName1 = list.files(dirPath, full.names=TRUE)[1] ## fileName2 = list.files(dirPath, full.names=TRUE)[2] ## binom=GOTHiC(fileName1,fileName2, sampleName="lymphoid_chr20", ## res=1000000, BSgenomeName="BSgenome.Hsapiens.UCSC.hg18", ## genome=BSgenome.Hsapiens.UCSC.hg18, ## restrictionSite="A^AGCTT", enzyme="HindIII" ,cistrans="all", filterdist=10000, ## DUPLICATETHRESHOLD=1, fileType="Table", parallel=FALSE, cores=NULL) ################################################### ### code chunk number 5: package_vignettes.Snw:114-119 (eval = FALSE) ################################################### ## dirPath <- system.file("extdata", package="HiCDataLymphoblast") ## fileName <- list.files(dirPath, full.names=TRUE)[4] ## restrictionFile <- list.files(dirPath, full.names=TRUE)[3] ## binom=GOTHiChicup(fileName, sampleName='lymphoid_chr20', res=1000000, ## restrictionFile, cistrans='all', parallel=FALSE, cores=NULL)