positionSequence {EpiTxDb}

R Documentation

Generate integer sequences from position information of Ranges

Description

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

Usage

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

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

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

## S4 method for signature '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)
gr2 <- GRanges("chr1:1-5:-")
positionSequence(gr)
# returns an IntegerList
grl <- GRangesList("1" = gr,"2" = gr,"3" = gr2) # must be named
positionSequence(grl)

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