keptProbaWin {strandCheckR} | R Documentation |
calculate the keeping probability of each window based on its positive/negative proportion
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 |
maxCov |
In the case that |
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