## ----results="hide", warning=FALSE, message=FALSE----------------------------- library(GenomicRanges) library(Motif2Site) library(BSgenome.Scerevisiae.UCSC.sacCer3) library(BSgenome.Ecoli.NCBI.20080805) ## ----warning=FALSE, message=FALSE, fig.width=10, fig.height=6----------------- yeastExampleFile = system.file("extdata", "YeastSampleMotif.bed", package="Motif2Site") YeastRegionsChIPseq <- Bed2Granges(yeastExampleFile) SequenceComparison <- compareMotifs2UserProvidedRegions( givenRegion=YeastRegionsChIPseq, motifs = c("TGATTSCAGGANT", "TGATTCCAGGANT", "TGATWSCAGGANT"), mismatchNumbers = c(1,0,2), genome="Scerevisiae", genomeBuild="sacCer3" ) SequenceComparison ## ----warning=FALSE, message=FALSE, fig.width=8, fig.height=6------------------ # Yeast artificial dataset for comparison bed files yeastExampleFile = system.file("extdata", "YeastSampleMotif.bed", package="Motif2Site") YeastRegionsChIPseq <- Bed2Granges(yeastExampleFile) bed1 <- system.file("extdata", "YeastBedFile1.bed", package="Motif2Site") bed2 <- system.file("extdata", "YeastBedFile2.bed", package="Motif2Site") BedFilesVector <- c(bed1, bed2) SequenceComparison <- compareBedFiless2UserProvidedRegions( givenRegion=YeastRegionsChIPseq, bedfiles = BedFilesVector, motifnames = c("YeastBed1", "YeastBed2") ) SequenceComparison ## ----message=FALSE, warning=FALSE--------------------------------------------- # FUR candidate motifs in NC_000913 E. coli FurMotifs = system.file("extdata", "FurMotifs.bed", package="Motif2Site") # ChIP-seq FUR fe datasets binding sites from user provided bed file # ChIP-seq datasets in bed single end format IPFe <- c(system.file("extdata", "FUR_fe1.bed", package="Motif2Site"), system.file("extdata", "FUR_fe2.bed", package="Motif2Site")) Inputs <- c(system.file("extdata", "Input1.bed", package="Motif2Site"), system.file("extdata", "Input2.bed", package="Motif2Site")) FURfeBedInputStats <- DetectBindingSitesBed(BedFile=FurMotifs, IPfiles=IPFe, BackgroundFiles=Inputs, genome="Ecoli", genomeBuild="20080805", DB="NCBI", expName="FUR_Fe_BedInput", format="BEDSE" ) FURfeBedInputStats # ChIP-seq FUR dpd datasets binding sites from user provided bed file # ChIP-seq datasets in bed single end format IPDpd <- c(system.file("extdata", "FUR_dpd1.bed", package="Motif2Site"), system.file("extdata", "FUR_dpd2.bed", package="Motif2Site")) FURdpdBedInputStats <- DetectBindingSitesBed(BedFile=FurMotifs, IPfiles=IPDpd, BackgroundFiles=Inputs, genome="Ecoli", genomeBuild="20080805", DB="NCBI", expName="FUR_Dpd_BedInput", format="BEDSE" ) FURdpdBedInputStats ## ----message=FALSE, warning=FALSE--------------------------------------------- # Granages region for motif search NC_000913_Coordiante <- GRanges(seqnames=Rle("NC_000913"), ranges = IRanges(1, 4639675)) # ChIP-seq FUR fe datasets binding sites from user provided string motif # ChIP-seq datasets in bed single end format FURfeStringInputStats <- DetectBindingSitesMotif(motif = "GWWTGAGAA", mismatchNumber = 1, IPfiles=IPFe, BackgroundFiles=Inputs, genome="Ecoli", genomeBuild="20080805", DB= "NCBI", expName="FUR_Fe_StringInput", format="BEDSE", GivenRegion = NC_000913_Coordiante ) FURfeStringInputStats ## ----message=FALSE, warning=FALSE--------------------------------------------- # Combine FUR binding sites from bed input into one table corMAT <- recenterBindingSitesAcrossExperiments( expLocations=c("FUR_Fe_BedInput","FUR_Dpd_BedInput"), experimentNames=c("FUR_Fe","FUR_Dpd"), expName="combinedFUR" ) corMAT FurTable <- read.table(file.path("combinedFUR","CombinedMatrix"), header = TRUE, check.names = FALSE ) FurBindingTotal <- GRanges(seqnames=Rle(FurTable[,1]), ranges = IRanges(FurTable[,2], FurTable[,3]) ) FurFe <- FurBindingTotal[which((FurTable$FUR_Fe_binding =="Binding")==TRUE)] FurDpd <- FurBindingTotal[which((FurTable$FUR_Dpd_binding =="Binding")==TRUE)] findOverlaps(FurFe,FurDpd) ## ----message=FALSE, warning=FALSE--------------------------------------------- # Differential binding sites across FUR conditions fe vs dpd diffFUR <- pairwisDifferential(tableOfCountsDir="combinedFUR", exp1="FUR_Fe", exp2="FUR_Dpd", FDRcutoff = 0.05, logFCcuttoff = 1 ) FeUp <- diffFUR[[1]] DpdUp <- diffFUR[[2]] TotalComparison <- diffFUR[[3]] head(TotalComparison) ## ----echo=FALSE, results='hide',message=FALSE--------------------------------- # Remove folders unlink("FUR_Fe_BedInput", recursive = TRUE) unlink("FUR_Dpd_BedInput", recursive = TRUE) unlink("FUR_Fe_StringInput", recursive = TRUE) unlink("combinedFUR", recursive = TRUE) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()