Mercurial > repos > testtool > annotate_peak

comparison annotate_peak/.Rhistory @ 18:6a9b9694acbf draft

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author testtool
date Mon, 20 Mar 2017 06:51:22 -0400
parents 53df7871db21
children
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17:982a01524118 18:6a9b9694acbf
134 TAB 134 TAB
135 csv_file<-("test-data/input.csv") 135 csv_file<-("test-data/input.csv")
136 TAB = read.csv(csv_file) 136 TAB = read.csv(csv_file)
137 TAB 137 TAB
138 ??bumphunter 138 ??bumphunter
139 ??toGranges
140 require("ChIPseeker", quietly = TRUE)
141 require("ChIPpeakAnno", quietly = TRUE)
142 options(warn = -1)
143 args <- commandArgs(trailingOnly = TRUE)
144 DMR = args[1]
145 annoPeakTable = args[2]
146 DMRInfo = read.table(
147 DMR,
148 header = FALSE,
149 sep = "\t",
150 stringsAsFactors = FALSE,
151 quote = ""
152 )
153 peaks <- GRanges(seqnames = DMRInfo[, 1],
154 ranges = IRanges
155 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
156 peaks[1:2]
157 DMR <- ("test-data/DMR.bed")
158 DMRInfo = read.table(
159 DMR,
160 header = FALSE,
161 sep = "\t",
162 stringsAsFactors = FALSE,
163 quote = ""
164 )
165 peaks <- GRanges(seqnames = DMRInfo[, 1],
166 ranges = IRanges
167 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
168 source("https://bioconductor.org/biocLite.R")
169 biocLite("EnsDb.Hsapiens.v75")
170 peaks <- toGRanges(seqnames = DMRInfo[, 1],
171 ranges = IRanges
172 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
173 peaks <- toGRanges(DMRInfo)
174 peaks <- toGRanges(seqnames = DMRInfo[, 1],
175 ranges = IRanges
176 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
177 DMR <- ("test-data/DMR.bed")
178 DMRInfo = read.table(
179 DMR,
180 header = FALSE,
181 sep = "\t",
182 stringsAsFactors = FALSE,
183 quote = ""
184 )
185 peaks <- toGRanges(seqnames = DMRInfo[, 1],
186 ranges = IRanges
187 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
188 peaks <- toGRanges(seqnames = DMRInfo[, 1], format=c("BED"), feature=c("gene"), header=FALSE,
189 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
190 peaks <- toGRanges(seqnames = DMRInfo[, 1], format=c("BED")
191 feature=c("gene") header=FALSE,(start = DMRInfo[, 2], end = DMRInfo[, 3]))
192 peaks <- toGRanges(seqnames = DMRInfo[, 1], format=c("BED"(start = DMRInfo[, 2], end = DMRInfo[, 3]))
193 peaks <- toGRanges(seqnames = DMRInfo[, 1], format=c("BED"(start = DMRInfo[, 2], end = DMRInfo[, 3]))
194 class(DMRInfo)
195 toGRanges(DMRInfo, seqnames = DMRInfo[, 1],(start = DMRInfo[, 2], end = DMRInfo[, 3]))
196 toGRanges(DMRInfo, seqnames = DMRInfo[, 1],(start = DMRInfo[, 2] end = DMRInfo[, 3]))
197 toGRanges(DMRInfo, seqnames = DMRInfo[, 1],start = DMRInfo[, 2], end = DMRInfo[, 3])
198 toGRanges(DMRInfo, seqnames = DMRInfo[, 1](start = DMRInfo[, 2], end = DMRInfo[, 3]))
199 toGRanges(DMRInfo, colNames = DMRInfo[, 1](start = DMRInfo[, 2], end = DMRInfo[, 3]))
200 peaks <- toGRanges(DMRInfo)
201 peaks <- GRanges(seqnames = DMRInfo[, 1],
202 ranges = IRanges
203 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
204 ??fread