Mercurial > repos > testtool > annotate_peak
comparison annotatePeak/.Rhistory @ 1:92387cb81962 draft
Uploaded
| author | testtool |
|---|---|
| date | Sat, 25 Feb 2017 11:18:27 -0500 |
| parents | 5d70366e7c6f |
| children | 7beb1a8f7cb0 |
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| 0:5d70366e7c6f | 1:92387cb81962 |
|---|---|
| 152 figure<-('test-data/figure.png') | 152 figure<-('test-data/figure.png') |
| 153 png(figure) | 153 png(figure) |
| 154 dev.off() | 154 dev.off() |
| 155 png(figure) | 155 png(figure) |
| 156 upsetplot(anno, vennpie=TRUE) | 156 upsetplot(anno, vennpie=TRUE) |
| 157 org.Hs.eg.db | |
| 158 ??org.Hs.eg.db | |
| 159 require("ChIPseeker", quietly = TRUE) | |
| 160 require("ChIPpeakAnno", quietly = TRUE) | |
| 161 DMRInfo = read.table( | |
| 162 DMR, | |
| 163 header = FALSE, | |
| 164 sep = "\t", | |
| 165 stringsAsFactors = FALSE, | |
| 166 quote = "" | |
| 167 ) | |
| 168 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1], | |
| 169 ranges = IRanges | |
| 170 (start = DMRInfo[, 2], end = DMRInfo[, 3])) | |
| 171 annotatePeak <- | |
| 172 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db")) | |
| 173 ??org.Hs.eg.db |