This function returns ranges that are defined relative to the strand-specific start and end sites of regions of interest (usually genes).
genebodies(
genelist,
start = 300L,
end = -300L,
fix.start = "start",
fix.end = "end",
min.window = 0L
)A GRanges object containing genes of interest.
Depending on fix.start, the distance from either the
strand-specific start or end site to begin the returned ranges. If
positive, the returned range will begin downstream of the reference
position; negative numbers are used to return sites upstream of the
reference. Set start = 0 to return the reference position.
Identical to the start argument, but defines the
strand-specific end position of returned ranges. end must be
downstream of start.
The reference point to use for defining the strand-specific
start positions of returned ranges, either "start" or "end".
The reference point to use for defining the strand-specific
end positions of returned ranges, either "start" or "end".
Cannot be set to "start" if fix.start = "end".
When fix.start = "start" and fix.end = "end",
min.window defines the minimum size (width) of a returned range.
However, when fix.end = fix.start, all returned ranges have the same
width, and min.window simply size-filters the input ranges.
A GRanges object that may be shorter than genelist due to
filtering of short ranges. For example, using the default arguments, genes
shorter than 600 bp would be removed.
Unlike
GenomicRanges::promoters,
distances can be defined to be upstream or downstream by changing the sign
of the argument, and both the start and end of the returned regions can be
defined in terms of the strand-specific start or end site of the input
ranges. For example, genebodies(txs, -50, 150, fix.end = "start") is
equivalent to promoters(txs, 50, 151) (the downstream edge is off by
1 because promoters keeps the downstream interval closed). The
default arguments return ranges that begin 300 bases downstream of the
original start positions, and end 300 bases upstream of the original end
positions.
data("txs_dm6_chr4") # load included transcript data
txs <- txs_dm6_chr4[c(1, 2, 167, 168)]
txs
#> GRanges object with 4 ranges and 2 metadata columns:
#> seqnames ranges strand | tx_name gene_id
#> <Rle> <IRanges> <Rle> | <character> <character>
#> [1] chr4 879-5039 + | FBtr0346692 FBgn0267363
#> [2] chr4 42774-43374 + | FBtr0344900 FBgn0266617
#> [3] chr4 5829-11765 - | FBtr0333684 FBgn0052011
#> [4] chr4 6374-11765 - | FBtr0089182 FBgn0052011
#> -------
#> seqinfo: 7 sequences from dm6 genome
#--------------------------------------------------#
# genebody regions from 300 bp after the TSS to
# 300 bp before the polyA site
#--------------------------------------------------#
genebodies(txs, 300, -300)
#> GRanges object with 4 ranges and 2 metadata columns:
#> seqnames ranges strand | tx_name gene_id
#> <Rle> <IRanges> <Rle> | <character> <character>
#> [1] chr4 1179-4739 + | FBtr0346692 FBgn0267363
#> [2] chr4 43074 + | FBtr0344900 FBgn0266617
#> [3] chr4 6129-11465 - | FBtr0333684 FBgn0052011
#> [4] chr4 6674-11465 - | FBtr0089182 FBgn0052011
#> -------
#> seqinfo: 7 sequences from dm6 genome
#--------------------------------------------------#
# promoter-proximal region from 50 bp upstream of
# the TSS to 100 bp downstream of the TSS
#--------------------------------------------------#
promoters(txs, 50, 101)
#> GRanges object with 4 ranges and 2 metadata columns:
#> seqnames ranges strand | tx_name gene_id
#> <Rle> <IRanges> <Rle> | <character> <character>
#> [1] chr4 829-979 + | FBtr0346692 FBgn0267363
#> [2] chr4 42724-42874 + | FBtr0344900 FBgn0266617
#> [3] chr4 11665-11815 - | FBtr0333684 FBgn0052011
#> [4] chr4 11665-11815 - | FBtr0089182 FBgn0052011
#> -------
#> seqinfo: 7 sequences from dm6 genome
genebodies(txs, -50, 100, fix.end = "start")
#> GRanges object with 4 ranges and 2 metadata columns:
#> seqnames ranges strand | tx_name gene_id
#> <Rle> <IRanges> <Rle> | <character> <character>
#> [1] chr4 829-979 + | FBtr0346692 FBgn0267363
#> [2] chr4 42724-42874 + | FBtr0344900 FBgn0266617
#> [3] chr4 11665-11815 - | FBtr0333684 FBgn0052011
#> [4] chr4 11665-11815 - | FBtr0089182 FBgn0052011
#> -------
#> seqinfo: 7 sequences from dm6 genome
#--------------------------------------------------#
# region from 500 to 1000 bp after the polyA site
#--------------------------------------------------#
genebodies(txs, 500, 1000, fix.start = "end")
#> GRanges object with 4 ranges and 2 metadata columns:
#> seqnames ranges strand | tx_name gene_id
#> <Rle> <IRanges> <Rle> | <character> <character>
#> [1] chr4 5539-6039 + | FBtr0346692 FBgn0267363
#> [2] chr4 43874-44374 + | FBtr0344900 FBgn0266617
#> [3] chr4 4829-5329 - | FBtr0333684 FBgn0052011
#> [4] chr4 5374-5874 - | FBtr0089182 FBgn0052011
#> -------
#> seqinfo: 7 sequences from dm6 genome