dot-keptProbaWin: Get the probability of being kept for each window
In UofABioinformaticsHub/rnaCleanR: 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 getWinOverlapEachReadFragment for positive reads
`winNegAlignments`	an object returned by getWinOverlapEachReadFragment 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 less than `minCov` reads, then it will be rejected regardless of 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 of 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

UofABioinformaticsHub/rnaCleanR documentation built on Aug. 11, 2021, 11:51 p.m.