BiocManager::install('chipseq')

For storing and manipulating genomic intervals and variables defined along a genome

library(GenomicRanges)

gr = GRanges(
    seqnames = c("chr1", "chr1", "chr2", "chr3"),
    ranges = IRanges(start = 1:4, 
                     end = 10:13, 
                    names = head(letters,4)),
    strand = c("-", "+", "+", "-"))

gr

GRanges object with 4 ranges and 0 metadata columns:
    seqnames    ranges strand
       <Rle> <IRanges>  <Rle>
  a     chr1      1-10      -
  b     chr1      2-11      +
  c     chr2      3-12      +
  d     chr3      4-13      -
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

gr[2]

GRanges object with 1 range and 0 metadata columns:
    seqnames    ranges strand
       <Rle> <IRanges>  <Rle>
  b     chr1      2-11      +
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

gr[2]

GRanges object with 1 range and 0 metadata columns:
    seqnames    ranges strand
       <Rle> <IRanges>  <Rle>
  b     chr1      2-11      +
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

gr[2:4]

GRanges object with 3 ranges and 0 metadata columns:
    seqnames    ranges strand
       <Rle> <IRanges>  <Rle>
  b     chr1      2-11      +
  c     chr2      3-12      +
  d     chr3      4-13      -
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

start(gr[2])

[1] 2

end(gr[2])

[1] 11

strand(gr[2])

factor-Rle of length 1 with 1 run
  Lengths: 1
  Values : +
Levels(3): + - *

gr[seqnames(gr)=="chr1"]

GRanges object with 2 ranges and 0 metadata columns:
    seqnames    ranges strand
       <Rle> <IRanges>  <Rle>
  a     chr1      1-10      -
  b     chr1      2-11      +
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

length(gr)

[1] 4

length(gr)

[1] 4

names(gr)

[1] "a" "b" "c" "d"

length(gr)

[1] 4

names(gr)

[1] "a" "b" "c" "d"

width(gr)

[1] 10 10 10 10

coverage(gr)

RleList of length 3
$chr1
integer-Rle of length 11 with 3 runs
  Lengths: 1 9 1
  Values : 1 2 1

$chr2
integer-Rle of length 12 with 2 runs
  Lengths:  2 10
  Values :  0  1

$chr3
integer-Rle of length 13 with 2 runs
  Lengths:  3 10
  Values :  0  1

run length encoding: a way of condensing ordered values into a smaller package

gum = c(T,T,T,T,F,F,F,T,T,T)
gum

 [1]  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE  TRUE

run length encoding: a way of condensing ordered values into a smaller package

gum = c(T,T,T,T,F,F,F,T,T,T)
gum

 [1]  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE  TRUE

rle.gum = rle(gum)
rle.gum

Run Length Encoding
  lengths: int [1:3] 4 3 3
  values : logi [1:3] TRUE FALSE TRUE

coverage(gr)

RleList of length 3
$chr1
integer-Rle of length 11 with 3 runs
  Lengths: 1 9 1
  Values : 1 2 1

$chr2
integer-Rle of length 12 with 2 runs
  Lengths:  2 10
  Values :  0  1

$chr3
integer-Rle of length 13 with 2 runs
  Lengths:  3 10
  Values :  0  1

gr

GRanges object with 4 ranges and 0 metadata columns:
    seqnames    ranges strand
       <Rle> <IRanges>  <Rle>
  a     chr1      1-10      -
  b     chr1      2-11      +
  c     chr2      3-12      +
  d     chr3      4-13      -
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

gr2 = GRanges(
    seqnames = c("chr1", "chr1", "chr2", "chr3"),
    ranges = IRanges(start = 1:4, 
                     end = 10:13, 
                    names = tail(letters,4)),
    strand = c("-", "+", "+", "-"))

gr2 = GRanges(
    seqnames = c("chr1", "chr1", "chr2", "chr3"),
    ranges = IRanges(start = 1:4, 
                     end = 10:13, 
                    names = tail(letters,4)),
    strand = c("-", "+", "+", "-"))
gr2

GRanges object with 4 ranges and 0 metadata columns:
    seqnames    ranges strand
       <Rle> <IRanges>  <Rle>
  w     chr1      1-10      -
  x     chr1      2-11      +
  y     chr2      3-12      +
  z     chr3      4-13      -
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

gr_list = GRangesList("gr1" = gr,"gr2" = gr2)

gr_list

GRangesList object of length 2:
$gr1
GRanges object with 4 ranges and 0 metadata columns:
    seqnames    ranges strand
       <Rle> <IRanges>  <Rle>
  a     chr1      1-10      -
  b     chr1      2-11      +
  c     chr2      3-12      +
  d     chr3      4-13      -
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

$gr2
GRanges object with 4 ranges and 0 metadata columns:
    seqnames    ranges strand
       <Rle> <IRanges>  <Rle>
  w     chr1      1-10      -
  x     chr1      2-11      +
  y     chr2      3-12      +
  z     chr3      4-13      -
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

gr_list$gr2

GRanges object with 4 ranges and 0 metadata columns:
    seqnames    ranges strand
       <Rle> <IRanges>  <Rle>
  w     chr1      1-10      -
  x     chr1      2-11      +
  y     chr2      3-12      +
  z     chr3      4-13      -
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

gr_list[2]

GRangesList object of length 1:
$gr2
GRanges object with 4 ranges and 0 metadata columns:
    seqnames    ranges strand
       <Rle> <IRanges>  <Rle>
  w     chr1      1-10      -
  x     chr1      2-11      +
  y     chr2      3-12      +
  z     chr3      4-13      -
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

• ppois
• dpois