Mercurial > repos > testtool > annotate_peak
comparison annotatePeak/.Rhistory @ 3:7beb1a8f7cb0 draft
Uploaded
| author | testtool |
|---|---|
| date | Mon, 27 Feb 2017 08:34:24 -0500 |
| parents | 92387cb81962 |
| children | e1c643f600d2 |
comparison
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| 2:be66730c5c3b | 3:7beb1a8f7cb0 |
|---|---|
| 169 ranges = IRanges | 169 ranges = IRanges |
| 170 (start = DMRInfo[, 2], end = DMRInfo[, 3])) | 170 (start = DMRInfo[, 2], end = DMRInfo[, 3])) |
| 171 annotatePeak <- | 171 annotatePeak <- |
| 172 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db")) | 172 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db")) |
| 173 ??org.Hs.eg.db | 173 ??org.Hs.eg.db |
| 174 DMR <- ("test-data/DMR.bed") | |
| 175 DMRInfo = read.table( | |
| 176 DMR, | |
| 177 header = FALSE, | |
| 178 sep = "\t", | |
| 179 stringsAsFactors = FALSE, | |
| 180 quote = "" | |
| 181 ) | |
| 182 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1], | |
| 183 ranges = IRanges | |
| 184 (start = DMRInfo[, 2], end = DMRInfo[, 3])) | |
| 185 ??GRanges | |
| 186 require("GenomicRanges", quietly = TRUE) | |
| 187 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1], | |
| 188 ranges = IRanges | |
| 189 (start = DMRInfo[, 2], end = DMRInfo[, 3])) | |
| 190 annotatePeak <- | |
| 191 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db")) | |
| 192 require("ChIPseeker", quietly = TRUE) | |
| 193 require("ChIPpeakAnno", quietly = TRUE) | |
| 194 annotatePeak <- | |
| 195 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db")) | |
| 196 annotatePeak <- | |
| 197 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db")) | |
| 198 write.csv(as.data.frame(annotatePeak), annoPeakTable, row.names = FALSE) | |
| 199 DMR <- ("test-data/DMR.bed") | |
| 200 DMRInfo = read.table( | |
| 201 DMR, | |
| 202 header = FALSE, | |
| 203 sep = "\t", | |
| 204 stringsAsFactors = FALSE, | |
| 205 quote = "" | |
| 206 ) | |
| 207 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1], | |
| 208 ranges = IRanges | |
| 209 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1], | |
| 210 ranges = IRanges | |
| 211 (start = DMRInfo[, 2], end = DMRInfo[, 3])) | |
| 212 ??GRanges | |
| 213 options(warn = -1) | |
| 214 args <- commandArgs(trailingOnly = TRUE) | |
| 215 DMR = args[1] | |
| 216 annoPeakTable = args[2] | |
| 217 DMR <- ("test-data/DMR.bed") | |
| 218 DMRInfo = read.table( | |
| 219 DMR, | |
| 220 header = FALSE, | |
| 221 sep = "\t", | |
| 222 stringsAsFactors = FALSE, | |
| 223 quote = "" | |
| 224 ) | |
| 225 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1], | |
| 226 ranges = IRanges | |
| 227 (start = DMRInfo[, 2], end = DMRInfo[, 3])) | |
| 228 ??GRanges | |
| 229 annotatePeak <- | |
| 230 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db")) |