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require(RNAseqData.HNRNPC.bam.chr14) | |
require(pasillaBamSubset) | |
require(Rsamtools) | |
bamFile <- untreated1_chr4() | |
# نلاحظ أن المجموعة اس هي المتواجدة هنا مما يدل على ان السلاسل احادية النهاية | |
quickBamFlagSummary(bamFile, main.groups.only = TRUE) | |
# group | nb of | nb of | mean / max | |
# of | records | unique | records per | |
# records | in group | QNAMEs | unique QNAME |
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require(pasillaBamSubset) | |
require(Rsamtools) | |
bamFile <- untreated1_chr4() | |
region <- GRanges("chr4",IRanges(100000L, 110000L)) | |
param <- ScanBamParam(which=region, what=scanBamWhat()) | |
mappedReads <- scanBam(bamFile, param=param) |
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require(pasillaBamSubset) | |
require(GenomicAlignments) | |
# BAM نقراء الملف | |
bamFile <- untreated1_chr4() | |
gReads <- readGAlignmentsFromBam(bamFile) | |
#GAlignments object with 204355 alignments and 0 metadata columns: | |
# seqnames strand cigar qwidth start end width njunc | |
# <Rle> <Rle> <character> <integer> <integer> <integer> <integer> <integer> | |
# [1] chr4 - 75M 75 892 966 75 0 | |
# [2] chr4 - 75M 75 919 993 75 0 |
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# rtracklayer يمكن استعمال الدوال الجاهزة في حزمة | |
encodePilotRegions <- import.bed("encodePilotRegion.bed") | |
encodePilotRegions | |
#GRanges object with 44 ranges and 1 metadata column: | |
# seqnames ranges strand | name | |
# <Rle> <IRanges> <Rle> | <character> | |
# [1] chr1 [151158061, 151658060] * | ENr231 | |
# [2] chr2 [ 51658705, 52158704] * | ENr112 | |
# [3] chr2 [118294574, 118794573] * | ENr121 | |
# [4] chr2 [220277346, 220777345] * | ENr331 |
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gr[1:2] | |
#GRanges object with 2 ranges and 1 metadata column: | |
# seqnames ranges strand | score | |
# <Rle> <IRanges> <Rle> | <numeric> | |
# [1] chr1 [ 130, 379] + | 0.0297835641540587 | |
# [2] chr1 [30050, 31349] + | 0.42395940516144 | |
# ------- | |
# seqinfo: 3 sequences from an unspecified genome; no seqlengths | |
start(gr) |
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# بعدة طرق GRanges يمكن انشاء | |
# مثلا يمكننا تحديد فقط المجالات الجينومية | |
gr <- GRanges(seqnames = c("chr1","chr1","chr2","chrX"), | |
ranges = IRanges(start = c(130,30050,4509,69098), | |
width= c(250,1300,400,590)), | |
strand = c("+","+","-","*")) | |
gr | |
#GRanges object with 4 ranges and 0 metadata columns: | |
# seqnames ranges strand | |
# <Rle> <IRanges> <Rle> |
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# ننشئ شعاع يحتوي على أرقام من 1 إلى 10 بطول 40 | |
x<- sort(sample(1:10,40,replace=T)) | |
head(x) | |
#[1] 1 1 1 1 1 1 | |
# Rle لحفضه | |
x <- Rle(x) | |
x | |
#integer-Rle of length 40 with 10 runs | |
# Lengths: 6 2 1 3 4 5 6 9 2 2 | |
# Values : 1 2 3 4 5 6 7 8 9 10 |
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range1 <- IRanges(start=c(10,50,300),end =c(60,90,456)) | |
range1 | |
#IRanges of length 3 | |
# start end width | |
#[1] 10 60 51 | |
#[2] 50 90 41 | |
#[3] 300 456 157 | |
reduce(range1) | |
#IRanges of length 2 |
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library(IRanges) | |
# يمكن انشاء مجموعة مجالات بتحديد نقطة البداية والنهاية | |
range1 <- IRanges(start=c(10,50,300),end =c(30,90,456)) | |
range1 | |
#IRanges of length 3 | |
# start end width | |
#[1] 10 30 21 | |
#[2] 50 90 41 | |
#[3] 300 456 157 |
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# نقوم بتحميل مواقع جزر السي بي جي لكامل الجينوم | |
dataURL <-"http://bios221.stanford.edu/data/model-based-cpg-islands-hg19.txt" | |
cpglocs=read.table(dataURL ,header=T) | |
# نختار فقظ الكروموزم رقم 8 | |
cpglocs8=cpglocs[which(cpglocs[,1]=="chr8"),2:3] | |
# الجدول يحتوي على أماكن بداية ونهاية كل جزيرة | |
head(cpglocs8) | |
# start end |
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