This man page documents intra range transformations of a linkSet object.
Usage
# S4 method for class 'linkSet'
trim(x, use.names = TRUE)
# S4 method for class 'linkSet'
resize(x, width, fix = "start", use.names = TRUE, ...)
# S4 method for class 'linkSet'
resizeRegions(
x,
width = 1000,
fix = "start",
use.names = TRUE,
region = "both",
...
)
# S4 method for class 'linkSet'
narrow(x, start = NA, end = NA, width = NA, use.names = TRUE)
# S4 method for class 'linkSet'
narrowRegions(
x,
start = NA,
end = NA,
width = NA,
use.names = TRUE,
region = "both"
)
# S4 method for class 'linkSet'
shift(x, shift = 0L, use.names = TRUE)
# S4 method for class 'linkSet'
shiftRegions(x, shift = 0L, use.names = TRUE, region = "both")
# S4 method for class 'linkSet'
flank(
x,
width,
start = TRUE,
both = FALSE,
use.names = TRUE,
ignore.strand = FALSE
)
# S4 method for class 'linkSet'
flankRegions(
x,
width,
start = TRUE,
both = FALSE,
use.names = TRUE,
ignore.strand = FALSE,
region = "both"
)
# S4 method for class 'linkSet'
promoters(x, upstream = 2000, downstream = 200, use.names = TRUE)
# S4 method for class 'linkSet'
promoterRegions(
x,
upstream = 2000,
downstream = 200,
use.names = TRUE,
region = "both"
)
# S4 method for class 'linkSet'
width(x)
# S4 method for class 'linkSet'
reduce(x, drop.empty.ranges = FALSE, ...)Examples
data(linkExample)
resize_bait <- resizeRegions(linkExample, width = 75, fix = "start", region = "bait")
resize_bait
#> linkSet object with 5 interactions and 1 metadata column:
#> bait seqnames_oe ranges_oe | anchor1.symbol
#> <character> <Rle> <IRanges> | <character>
#> [1] Gene1 --- chr1 50-59 | Gene1
#> [2] Gene1 --- chr2 150-159 | Gene1
#> [3] Gene2 --- chr2 250-259 | Gene2
#> [4] Gene3 --- chr4 350-359 | Gene3
#> [5] Gene3 --- chr4 450-459 | Gene3
#> -------
#> regions: 10 ranges and 0 metadata columns
#> seqinfo: 4 sequences from an unspecified genome; no seqlengths
narrow_bait <- narrowRegions(linkExample, start = 10, width = 40, region = "bait")
#> Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord, allow.nonnarrowing, PACKAGE = "IRanges"): solving row 1: 'allow.nonnarrowing' is FALSE and the solved end (49) is > refwidth
narrow_bait
#> Error in eval(expr, envir, enclos): object 'narrow_bait' not found
shift_oe <- shiftRegions(linkExample, shift = 10, region = "oe")
shift_oe
#> linkSet object with 5 interactions and 1 metadata column:
#> bait seqnames_oe ranges_oe | anchor1.symbol
#> <character> <Rle> <IRanges> | <character>
#> [1] Gene1 --- chr1 60-69 | Gene1
#> [2] Gene1 --- chr2 160-169 | Gene1
#> [3] Gene2 --- chr2 260-269 | Gene2
#> [4] Gene3 --- chr4 360-369 | Gene3
#> [5] Gene3 --- chr4 460-469 | Gene3
#> -------
#> regions: 10 ranges and 0 metadata columns
#> seqinfo: 4 sequences from an unspecified genome; no seqlengths
flank_bait <- flankRegions(linkExample, width = 100, start = TRUE, both = FALSE, use.names = TRUE, ignore.strand = FALSE, region = "bait")
flank_bait
#> linkSet object with 5 interactions and 1 metadata column:
#> bait seqnames_oe ranges_oe | anchor1.symbol
#> <character> <Rle> <IRanges> | <character>
#> [1] Gene1 --- chr1 50-59 | Gene1
#> [2] Gene1 --- chr2 150-159 | Gene1
#> [3] Gene2 --- chr2 250-259 | Gene2
#> [4] Gene3 --- chr4 350-359 | Gene3
#> [5] Gene3 --- chr4 450-459 | Gene3
#> -------
#> regions: 10 ranges and 0 metadata columns
#> seqinfo: 4 sequences from an unspecified genome; no seqlengths
width(linkExample)
#> $bait
#> [1] 10 10 10 10 10
#>
#> $oe
#> [1] 10 10 10 10 10
#>