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sirusb/Biostrings_Views.r

Last active August 29, 2015 14:13
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Example of using Biostrings views
Raw
Biostrings_Views.r
library(Biostrings)
library(BSgenome.Hsapiens.UCSC.hg19)
#نأخذ الكروموزوم 1 كمثال
Hsapiens$chr1
# 249250621-letter "DNAString" instance
#seq: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
# لنفرض أننا مهتمين بسلسلة الجينات ABCA4, ACADM و GBA
genes <- Views(Hsapiens$chr1,
start = c(93992836, 75724346, 155234447 ),
end=c(94121148, 75763678, 155244861))
genes
# Views on a 249250621-letter DNAString subject
#subject: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
#views:
# start end width
#[1] 93992836 94121148 128313 [AAATTGCTAACTGCTAGGGAAC...AATTAGCAAATACCTTTGCCTC]
#[2] 75724346 75763678 39333 [AGCGTTTGAGCTCCAATAAGGG...AACAACAACAAAAATGTCTCTT]
#[3] 155234447 155244861 10415 [TCTGGTGCTCGGTAATGGCGAG...GTGGCTCATGCCTGTAATCCCA]
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