GRanges construction

GRanges_construction.r

# 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>
#  [1]     chr1 [  130,   379]      +
#  [2]     chr1 [30050, 31349]      +
#  [3]     chr2 [ 4509,  4908]      -
#  [4]     chrX [69098, 69687]      *
#  -------
#  seqinfo: 3 sequences from an unspecified genome; no seqlengths

# mcols يمكن اظافة البيانات الوصفية باستعمال دالة 
mcols(gr) <- DataFrame(score = runif(4))
gr
#GRanges object with 4 ranges and 1 metadata column:
#      seqnames         ranges strand |             score
#         <Rle>      <IRanges>  <Rle> |         <numeric>
#  [1]     chr1 [  130,   379]      + | 0.779228801373392
#  [2]     chr1 [30050, 31349]      + | 0.325288600986823
#  [3]     chr2 [ 4509,  4908]      - | 0.609552363865077
#  [4]     chrX [69098, 69687]      * | 0.229161157971248
#  -------
#  seqinfo: 3 sequences from an unspecified genome; no seqlengths

# او يمكننا اظافتها عند الانشاء, يمكن اعطاء اي اسم للحقول المضافة

gr <- GRanges(seqnames = c("chr1","chr1","chr2","chrX"),
              ranges = IRanges(start = c(130,30050,4509,69098),
                               width= c(250,1300,400,590)),
              strand = c("+","+","-","*"),
              score = runif(4))
gr
#GRanges object with 4 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
#  [3]     chr2 [ 4509,  4908]      - |  0.112338428385556
#  [4]     chrX [69098, 69687]      * |  0.800393168348819
#  -------
#  seqinfo: 3 sequences from an unspecified genome; no seqlengths