getWinFromIRanges: Get the Ranges of Sliding Windows from an IRanges object
In strandCheckR: Calculate strandness information of a bam file

Description Usage Arguments Details Value

Get the Ranges of Sliding Windows from an IRanges object

1 2	getWinFromIRanges(x, winWidth = 1000L, winStep = 100L, readProp = 0.5, maxWin = Inf)

`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

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.

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

strandCheckR documentation built on Nov. 8, 2020, 7:02 p.m.