### R code from vignette source 'vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.Rnw' ################################################### ### code chunk number 1: ChIPpeakAnno.Rnw:35-40 ################################################### library(ChIPpeakAnno) data(myPeakList) data(TSS.human.NCBI36) annotatedPeak = annotatePeakInBatch(myPeakList[1:6,], AnnotationData=TSS.human.NCBI36) as.data.frame(annotatedPeak) ################################################### ### code chunk number 2: ChIPpeakAnno.Rnw:52-69 ################################################### myPeak1 = RangedData(IRanges(start=c(967654, 2010897, 2496704, 3075869, 3123260 ,3857501,201089,1543200,1557200,1563000,1569800,167889600), end= c(967754, 2010997, 2496804, 3075969, 3123360 ,3857601,201089,1555199, 1560599,1565199,1573799,167893599),names=c("Site1", "Site2", "Site3", "Site4", "Site5", "Site6", "Site7","Site8","Site9","Site10","Site11","Site12")), space=c("1", "2", "3", "4", "5", "6","2","6","6","6","6","5")) TFbindingSites = RangedData(IRanges(start=c(967659, 2010898, 2496700, 3075866, 3123260 ,3857500, 96765, 201089, 249670, 307586, 312326 ,385750,1549800,1554400, 1565000,1569400,167888600), end=c(967869, 2011108, 2496920,3076166,3123470, 3857780, 96985, 201299, 249890, 307796,312586,385960,1550599,1560799,1565399, 1571199,167888999), names=c("t1", "t2", "t3", "t4", "t5", "t6","t7", "t8", "t9", "t10", "t11", "t12","t13","t14","t15","t16","t17")), space=c("1", "2", "3", "4", "5", "6","1", "2", "3", "4", "5", "6","6","6","6","6","5"), strand=c(1,1,1,1,1,1,-1,-1,-1,-1,-1,-1,1,1,1,1,1)) annotatedPeak2 = annotatePeakInBatch(myPeak1, AnnotationData=TFbindingSites) pie(table(as.data.frame(annotatedPeak2)$insideFeature)) as.data.frame(annotatedPeak2) ################################################### ### code chunk number 3: ChIPpeakAnno.Rnw:82-100 ################################################### peaks1 = RangedData(IRanges(start=c(967654, 2010897, 2496704, 3075869, 3123260 ,3857501,201089,1543200,1557200,1563000, 1569800,167889600), end= c(967754, 2010997, 2496804, 3075969, 3123360 ,3857601,201089,1555199,1560599,1565199,1573799, 167893599),names=c("Site1", "Site2", "Site3", "Site4", "Site5", "Site6", "Site7","Site8","Site9","Site10","Site11","Site12")), space=c("1", "2", "3", "4", "5", "6","2","6","6","6","6","5"),strand=as.integer(1)) peaks2 = RangedData(IRanges(start=c(967659, 2010898, 2496700, 3075866, 3123260 , 3857500, 96765, 201089, 249670, 307586, 312326 ,385750,1549800,1554400,1565000, 1569400,167888600), end=c(967869, 2011108, 2496920,3076166,3123470,3857780, 96985, 201299, 249890, 307796,312586,385960,1550599,1560799,1565399, 1571199,167888999), names=c("t1", "t2", "t3", "t4", "t5", "t6","t7", "t8", "t9", "t10", "t11", "t12","t13","t14","t15","t16","t17")), space=c("1", "2", "3", "4", "5", "6","1", "2", "3", "4", "5", "6","6","6","6","6","5"), strand=c(1,1,1,1,1,1,-1,-1,-1,-1,-1,-1,1,1,1,1,1)) t1 =findOverlappingPeaks(peaks1, peaks2, maxgap=1000, minoverlap =20,select="first", NameOfPeaks1="TF1", NameOfPeaks2="TF2", annotate=1) ################################################### ### code chunk number 4: ChIPpeakAnno.Rnw:106-109 ################################################### overlappingPeaks = t1$OverlappingPeaks overlappingPeaks pie(table(overlappingPeaks$overlapFeature)) ################################################### ### code chunk number 5: ChIPpeakAnno.Rnw:114-115 ################################################### as.data.frame(t1$MergedPeaks) ################################################### ### code chunk number 6: ChIPpeakAnno.Rnw:122-123 ################################################### as.data.frame(t1$Peaks1withOverlaps) ################################################### ### code chunk number 7: ChIPpeakAnno.Rnw:130-131 ################################################### as.data.frame(t1$Peaks2withOverlaps) ################################################### ### code chunk number 8: ChIPpeakAnno.Rnw:136-146 ################################################### peaks3 = RangedData(IRanges(start=c(967859, 2010868, 2496500, 3075966, 3123460 ,3851500, 96865, 201189, 249600, 307386), end=c(967969, 2011908, 2496720,3076166,3123470,3857680, 96985, 201299, 249890, 307796), names=c("p1", "p2", "p3", "p4", "p5", "p6","p7", "p8", "p9", "p10")), space=c("1", "2", "3", "4", "5", "6","1", "2", "3", "4"), strand= c(1,1,1,1,1,1,-1,-1,-1,-1)) findOverlappingPeaks(findOverlappingPeaks(peaks1, peaks2, maxgap=1000, minoverlap = 1, select= "first",NameOfPeaks1="TF1", NameOfPeaks2="TF2")$Peaks1withOverlap, peaks3, maxgap=1000, minoverlap = 1, select="first", NameOfPeaks1="TF1TF2", NameOfPeaks2="TF3")$Peaks1withOverlap ################################################### ### code chunk number 9: ChIPpeakAnno.Rnw:152-154 ################################################### makeVennDiagram(RangedDataList(peaks1, peaks2), NameOfPeaks=c("TF1", "TF2"), maxgap=0, minoverlap =1, totalTest=100, cex = 1, counts.col = "red",useFeature=FALSE) ################################################### ### code chunk number 10: ChIPpeakAnno.Rnw:163-167 ################################################### peaks = RangedData(IRanges(start=c(100, 500), end=c(300, 600), names=c("peak1", "peak2")), space=c("NC_008253", "NC_010468")) library(BSgenome.Ecoli.NCBI.20080805) peaksWithSequences = getAllPeakSequence(peaks, upstream = 20, downstream = 20, genome = Ecoli) ################################################### ### code chunk number 11: ChIPpeakAnno.Rnw:174-175 ################################################### write2FASTA(peaksWithSequences,"test.fa") ################################################### ### code chunk number 12: ChIPpeakAnno.Rnw:198-199 ################################################### data(enrichedGO) ################################################### ### code chunk number 13: ChIPpeakAnno.Rnw:205-206 ################################################### enrichedGO$bp[1:6,] ################################################### ### code chunk number 14: ChIPpeakAnno.Rnw:213-214 ################################################### enrichedGO$mf[1:6,] ################################################### ### code chunk number 15: ChIPpeakAnno.Rnw:221-222 ################################################### enrichedGO$cc ################################################### ### code chunk number 16: ChIPpeakAnno.Rnw:231-238 ################################################### data(myPeakList) data(TSS.human.NCBI36) annotatedBDP = peaksNearBDP(myPeakList[1:10,], AnnotationData=TSS.human.NCBI36, MaxDistance=5000,PeakLocForDistance = "middle", FeatureLocForDistance = "TSS") annotatedBDP$peaksWithBDP c(annotatedBDP$percentPeaksWithBDP, annotatedBDP$n.peaks, annotatedBDP$n.peaksWithBDP) ################################################### ### code chunk number 17: ChIPpeakAnno.Rnw:247-252 ################################################### peaks = RangedData(IRanges(start=c(100, 500), end=c(300, 600), names=c("peak1", "peak2")), space=c("NC_008253", "NC_010468")) filepath =system.file("extdata", "examplePattern.fa", package="ChIPpeakAnno") library(BSgenome.Ecoli.NCBI.20080805) summarizePatternInPeaks(patternFilePath=filepath, format="fasta", skip=0L, BSgenomeName=Ecoli, peaks=peaks) ################################################### ### code chunk number 18: ChIPpeakAnno.Rnw:261-265 ################################################### data(annotatedPeak) library(org.Hs.eg.db) addGeneIDs(annotatedPeak[1:6,],"org.Hs.eg.db",c("symbol")) addGeneIDs(annotatedPeak$feature[1:6],"org.Hs.eg.db",c("symbol")) ################################################### ### code chunk number 19: ChIPpeakAnno.Rnw:282-283 ################################################### sessionInfo()