# HG changeset patch # User kpbioteam # Date 1525267443 14400 # Node ID efd9e1315ed5e51cdbe9ec5a5761ac5cd5d46ac3 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty diff -r 000000000000 -r efd9e1315ed5 annoTab.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annoTab.txt Wed May 02 09:24:03 2018 -0400 @@ -0,0 +1,13181 @@ +"seqnames" "start" "end" "width" "strand" "value_pos" "peak" "feature" "feature.ranges.start" "feature.ranges.end" "feature.ranges.width" "feature.strand" "distance" "insideFeature" "distanceToSite" "gene_name" +"chrX" 68047520 68049085 1566 "*" 0.521502742570152 "X1" "ENSG00000090776" 68048840 68061990 13151 "+" 0 "overlapStart" 0 "EFNB1" +"chrX" 48754982 48755797 816 "*" 0.519942832634712 "X2" "ENSG00000102103" 48755195 48760420 5226 "+" 0 "overlapStart" 0 "PQBP1" +"chrX" 48754982 48755797 816 "*" 0.519942832634712 "X2" "ENSG00000126768" 48750730 48755426 4697 "-" 0 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249120576 249120642 67 "+" 124 "upstream" 124 "MIR3124" +"chr1" 249120451 249120451 1 "*" 0.5 "X16709" "ENSG00000175137" 249104648 249120832 16185 "-" 0 "inside" 380 "SH3BP5L" +"chrX" 15872521 15872521 1 "*" 0.5 "X16710" "ENSG00000182287" 15843929 15873054 29126 "-" 0 "inside" 532 "AP1S2" +"chrX" 24167821 24167821 1 "*" 0.5 "X16711" "ENSG00000005889" 24167290 24234372 67083 "+" 0 "inside" 530 "ZFX" +"chrX" 24167821 24167821 1 "*" 0.5 "X16711" "ENSG00000234230" 24164342 24167771 3430 "-" 49 "upstream" 49 "ZFX-AS1" diff -r 000000000000 -r efd9e1315ed5 chipeakanno_annopeaks.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chipeakanno_annopeaks.R Wed May 02 09:24:03 2018 -0400 @@ -0,0 +1,23 @@ +require("ChIPpeakAnno", quietly = TRUE) +require("EnsDb.Hsapiens.v75", quietly = TRUE) +require("rtracklayer", quietly = TRUE) + +options(warn = -1) +options("download.file.method"="wget") + +args <- commandArgs(trailingOnly = TRUE) + +input1 = args[1] +input2 = args[2] +input3 = as.numeric(args[3]) +input4 = as.numeric(args[4]) +output1 = args[5] + +peaks <- get(load(input1)) + +annoData <- toGRanges(EnsDb.Hsapiens.v75) +seqlevelsStyle(peaks) <- seqlevelsStyle(annoData) + + anno <- annoPeaks(peaks, annoData=annoData, bindingType =c(input2), bindingRegion=c(input3, input4)) + + write.table(anno, file= output1, row.names = FALSE) diff -r 000000000000 -r efd9e1315ed5 chipeakanno_annopeaks.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chipeakanno_annopeaks.xml Wed May 02 09:24:03 2018 -0400 @@ -0,0 +1,58 @@ + + annotate peaks by annoGR object in the given range + + bioconductor-chippeakanno + bioconductor-ensdb.hsapiens.v75 + bioconductor-rtracklayer + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.18129/B9.bioc.ChIPpeakAnno + + diff -r 000000000000 -r efd9e1315ed5 dmr.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dmr.bed Wed May 02 09:24:03 2018 -0400 @@ -0,0 +1,16720 @@ +"seqnames" "start" "end" "width" "strand" "value_pos" +"1" 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"inside" 173 "RP4-559A3.7" +"chr1" 226111804 226111804 1 "*" 0.5 "X16691" "ENSG00000143811" 226107578 226111978 4401 "-" 0 "inside" 173 "PYCR2" +"chr1" 226496911 226496911 1 "*" 0.5 "X16692" "ENSG00000183814" 226418850 226497570 78721 "-" 0 "inside" 658 "LIN9" +"chr1" 228290868 228290868 1 "*" 0.5 "X16693" "ENSG00000143793" 228288427 228293112 4686 "-" 0 "inside" 2243 "C1orf35" +"chr1" 229478159 229478159 1 "*" 0.5 "X16694" "ENSG00000154429" 229456758 229479041 22284 "-" 0 "inside" 881 "CCSAP" +"chr1" 229694604 229694604 1 "*" 0.5 "X16695" "ENSG00000135776" 229652329 229694442 42114 "-" 161 "upstream" 161 "ABCB10" +"chr1" 231113872 231113872 1 "*" 0.5 "X16696" "ENSG00000143643" 231041989 231114621 72633 "-" 0 "inside" 748 "TTC13" +"chr1" 231113872 231113872 1 "*" 0.5 "X16696" "ENSG00000173409" 231114727 231136341 21615 "+" 854 "upstream" 854 "ARV1" +"chr1" 231376624 231376624 1 "*" 0.5 "X16697" "ENSG00000143633" 231359509 231376933 17425 "-" 0 "inside" 308 "C1orf131" +"chr1" 231376624 231376624 1 "*" 0.5 "X16697" "ENSG00000116906" 231376953 231413719 36767 "+" 328 "upstream" 328 "GNPAT" +"chr1" 231376895 231376895 1 "*" 0.5 "X16698" "ENSG00000143633" 231359509 231376933 17425 "-" 0 "inside" 37 "C1orf131" +"chr1" 231376895 231376895 1 "*" 0.5 "X16698" "ENSG00000116906" 231376953 231413719 36767 "+" 57 "upstream" 57 "GNPAT" +"chr1" 234509775 234509775 1 "*" 0.5 "X16699" "ENSG00000168275" 234509202 234519795 10594 "+" 0 "inside" 572 "COA6" +"chr1" 234509775 234509775 1 "*" 0.5 "X16699" "ENSG00000231663" 234508553 234509339 787 "-" 435 "upstream" 435 "RP5-827C21.4" +"chr1" 234748618 234748618 1 "*" 0.5 "X16701" "ENSG00000168264" 234740015 234745271 5257 "-" 3346 "upstream" 3346 "IRF2BP2" +"chr1" 235530811 235530811 1 "*" 0.5 "X16702" "ENSG00000116957" 235530675 235612283 81609 "+" 0 "inside" 135 "TBCE" +"chr1" 243418761 243418761 1 "*" 0.5 "X16703" "ENSG00000143702" 243287730 243418650 130921 "-" 110 "upstream" 110 "CEP170" +"chr1" 243418761 243418761 1 "*" 0.5 "X16703" "ENSG00000054282" 243419320 243663394 244075 "+" 558 "upstream" 558 "SDCCAG8" +"chr1" 244999141 244999141 1 "*" 0.5 "X16704" "ENSG00000203667" 244998624 245008359 9736 "+" 0 "inside" 516 "COX20" +"chr1" 245025960 245025960 1 "*" 0.5 "X16705" "ENSG00000153187" 245014468 245027844 13377 "-" 0 "inside" 1883 "HNRNPU" +"chr1" 245025960 245025960 1 "*" 0.5 "X16705" "ENSG00000273175" 245028040 245028574 535 "+" 2079 "upstream" 2079 "RP11-11N7.4" +"chr1" 245028075 245028075 1 "*" 0.5 "X16706" "ENSG00000153187" 245014468 245027844 13377 "-" 230 "upstream" 230 "HNRNPU" +"chr1" 245028075 245028075 1 "*" 0.5 "X16706" "ENSG00000273175" 245028040 245028574 535 "+" 0 "inside" 34 "RP11-11N7.4" +"chr1" 247094386 247094386 1 "*" 0.5 "X16707" "ENSG00000153207" 247002400 247095280 92881 "-" 0 "inside" 893 "AHCTF1" +"chr1" 247495250 247495250 1 "*" 0.5 "X16708" "ENSG00000162714" 247460714 247495148 34435 "-" 101 "upstream" 101 "ZNF496" +"chr1" 249120451 249120451 1 "*" 0.5 "X16709" "ENSG00000264500" 249120576 249120642 67 "+" 124 "upstream" 124 "MIR3124" +"chr1" 249120451 249120451 1 "*" 0.5 "X16709" "ENSG00000175137" 249104648 249120832 16185 "-" 0 "inside" 380 "SH3BP5L" +"chrX" 15872521 15872521 1 "*" 0.5 "X16710" "ENSG00000182287" 15843929 15873054 29126 "-" 0 "inside" 532 "AP1S2" +"chrX" 24167821 24167821 1 "*" 0.5 "X16711" "ENSG00000005889" 24167290 24234372 67083 "+" 0 "inside" 530 "ZFX" +"chrX" 24167821 24167821 1 "*" 0.5 "X16711" "ENSG00000234230" 24164342 24167771 3430 "-" 49 "upstream" 49 "ZFX-AS1" diff -r 000000000000 -r efd9e1315ed5 test-data/peaks.rdata Binary file test-data/peaks.rdata has changed