Mercurial > repos > testtool > annotate_peak

comparison annotatePeak/.Rhistory @ 3:7beb1a8f7cb0 draft

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Uploaded
author testtool
date Mon, 27 Feb 2017 08:34:24 -0500
parents 92387cb81962
children e1c643f600d2
comparison
equal deleted inserted replaced
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"))