Generate integer sequences from position information of Ranges

positionSequence generates sequences of integer values along the range information of x. This can be used for navigating specific positions on a range information.

positionSequence(x, order = FALSE, decreasing = FALSE)

# S4 method for Ranges
positionSequence(x, order = FALSE, decreasing = FALSE)

# S4 method for RangesList
positionSequence(x, order = FALSE, decreasing = FALSE)

# S4 method for Ranges
as.integer(x)

Arguments

x

a Ranges object, like a GRanges or IRanges, or a RangesList object, like a GRangesList or IRangesList

order

TRUE or FALSE: Should the position be ordered? (default: order = FALSE)

decreasing

TRUE or FALSE: If order = TRUE Should the position be ordered in a decreasing order? (default: order = FALSE)

Value

a integer vector if x is a

GRanges object and a

IntegerList if x is a

GRangesList

Examples

library(GenomicRanges)
# Returns an integer vector
gr <- GRanges("chr1:1-5:+")
positionSequence(gr)
#> [1] 1 2 3 4 5
gr2 <- GRanges("chr1:1-5:-")
positionSequence(gr)
#> [1] 1 2 3 4 5
# returns an IntegerList
grl <- GRangesList("1" = gr,"2" = gr,"3" = gr2) # must be named
positionSequence(grl)
#> IntegerList of length 3
#> [["1"]] 1 2 3 4 5
#> [["2"]] 1 2 3 4 5
#> [["3"]] 5 4 3 2 1