keptProbaWin: get the probability of begin kept for each window
In strandCheckR: Calculate strandness information of a bam file

calculate the keeping probability of each window based on its positive/negative proportion

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keptProbaWin(winPosAlignments, winNegAlignments, winWidth, winStep, threshold,
pvalueThreshold, errorRate, mustKeepWin, minCov, maxCov, getWin,
useCoverage = FALSE)

`winPosAlignments`	an object returned by getWinOfAlignments for positive reads
`winNegAlignments`	an object returned by getWinOfAlignments for negative reads
`winWidth`	the width of the sliding window, 1000 by default.
`winStep`	the winStep length to sliding the window, 100 by default.
`threshold`	the strand proportion threshold to test whether to keep a window or not.
`pvalueThreshold`	threshold of p-value
`errorRate`	the probability that an RNA read takes the false strand. 0.01 by default
`mustKeepWin`	the windows that must be kept regardless their strand proportion
`minCov`	In the case that `useCoverage=FALSE`, if a window has least than `minCov` reads, then it will be rejected regardless the strand proportion. For the case that `useCoverage=TRUE`, if a window has max coverage least than `minCov`, then it will be rejected. 0 by default
`maxCov`	In the case that `useCoverage=FALSE`, if a window has more than `maxCov` reads, then it will be kept regardless the strand proportion. For the case that `useCoverage=TRUE`, if a window has max coverage more than `maxCov`, then it will be kept. If 0 then it doesn't have effect on selecting window. 0 by default.
`getWin`	if TRUE, the function will return a data frame containing the information of all windows. It's FALSE by default.
`useCoverage`	if TRUE, then the strand information in each window corresponds to the sum of coverage coming from positive/negative reads; and not the number of positive/negative reads as default.

A list of 2 numeric-Rle objects containing keeping probability of each +/- alignments. If getWin=TRUE then the list contains an additional DataFrame for the number of reads and coverage of the input window +/- alignments

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