Slide 8
Slide 8 text
CpG配列データの準備
コード
# データの読み込み
filePath=system.file("extdata",
"cpgi.hg19.chr21.bed",
package="compGenomRData")
cpgi.df = read.table(filePath, header = FALSE,
stringsAsFactors=FALSE)
# データの前処理(余分なデータを含めない)
cpgi.df =cpgi.df [grep("_",cpgi.df[,1],invert=TRUE),]
# データフレームから、GRangeオブジェクトへ変換
cpgi.gr=GRanges(seqnames=cpgi.df[,1],
ranges=IRanges(start=cpgi.df[,2],
end=cpgi.df[,3]))
出力結果
> cpgi.gr
GRanges object with 205 ranges and 0 metadata columns:
seqnames ranges strand
[1] chr21 9825442-9826296 *
[2] chr21 9909011-9909218 *
[3] chr21 9968264-9968620 *
[4] chr21 10989913-10991413 *
[5] chr21 14409412-14410501 *
... ... ... ...
[201] chr21 47918497-47918728 *
[202] chr21 48018542-48018791 *
[203] chr21 48055199-48056060 *
[204] chr21 48068517-48068808 *
[205] chr21 48081241-48081849 *
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