Importing_bed.r

# 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
#   [5]     chr2 [234491825, 234991888]      *   |      ENr131
#   ...      ...                    ...    ... ...         ...
#  [40]    chr19   [54331773, 55332648]      *   |      ENm007
#  [41]    chr20   [33841513, 34341514]      *   |      ENr333
#  [42]    chr21   [33746366, 35442351]      *   |      ENm005
#  [43]    chr21   [40322597, 40822596]      *   |      ENr133
#  [44]    chr22   [31803954, 33503953]      *   |      ENm004
#  -------
#  seqinfo: 21 sequences from an unspecified genome; no seqlengths

# أو يمكن تحضير كل شيء يدويا
df <- read.table("encodePilotRegion.bed",sep="\t")
head(df)
#    V1        V2        V3     V4
#1 chr1 151158060 151658060 ENr231
#2 chr2  51658704  52158704 ENr112
#3 chr2 118294573 118794573 ENr121
#4 chr2 220277345 220777345 ENr331
#5 chr2 234491824 234991888 ENr131
#6 chr4 118246655 118746655 ENr113

encodePilotRegions2
#GRanges object with 44 ranges and 1 metadata column:
#       seqnames                 ranges strand   |     name
#          <Rle>              <IRanges>  <Rle>   | <factor>
#   [1]     chr1 [151158060, 151658060]      *   |   ENr231
#   [2]     chr2 [ 51658704,  52158704]      *   |   ENr112
#   [3]     chr2 [118294573, 118794573]      *   |   ENr121
#   [4]     chr2 [220277345, 220777345]      *   |   ENr331
#   [5]     chr2 [234491824, 234991888]      *   |   ENr131
#   ...      ...                    ...    ... ...      ...
#  [40]    chr19   [54331772, 55332648]      *   |   ENm007
#  [41]    chr20   [33841512, 34341514]      *   |   ENr333
#  [42]    chr21   [33746365, 35442351]      *   |   ENm005
#  [43]    chr21   [40322596, 40822596]      *   |   ENr133
#  [44]    chr22   [31803953, 33503953]      *   |   ENm004
#  -------
#  seqinfo: 21 sequences from an unspecified genome; no seqlengths