sirusb

# 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>

sirusb

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)

sirusb

# 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

sirusb

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

sirusb

require(pasillaBamSubset)
require(Rsamtools)
bamFile <- untreated1_chr4()
region <- GRanges("chr4",IRanges(100000L, 110000L))
param <- ScanBamParam(which=region, what=scanBamWhat())
mappedReads <- scanBam(bamFile, param=param)

sirusb

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