getWinFromIRanges: Get the Ranges of Sliding Windows from an IRanges object

Description Usage Arguments Details Value

View source: R/getWinFromIRanges.R

Description

Get the Ranges of Sliding Windows from an IRanges object

Usage

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getWinFromIRanges(x, winWidth = 1000L, winStep = 100L, readProp = 0.5,
maxWin = Inf)

Arguments

x

an IRanges object containing the start and end position of each read fragment

winWidth

The width of each window

winStep

The step size for sliding the window

readProp

A read is considered to be included in a window if at least readProp of it is in the window. Specified as a proportion.

maxWin

The maximum window ID

Details

This finds the windows that overlap each fragment of a read and returns a range containing this list of windows for each read fragment. This allows the total number of read fragments within a window to be calculated simply using coverage.

Value

An IRanges object containing the index of the windows containing each read fragment


strandCheckR documentation built on Nov. 1, 2018, 2:26 a.m.