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Do not abort integration (over het-het distances) on errors, but warn about them 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4855 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2010-12-16 17:20:25 +00:00
parent 8ab4704b4c
commit 6310a524d9
1 changed files with 5 additions and 1 deletions
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6
R/phasing/RBP_theoretical.R
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@ -141,7 +141,11 @@ pDirectlyPhaseHetPair <- function(meanDepth, nReadsToPhase, L, theta, Fm, Fs) {
MIN_DISTANCE = 0 MIN_DISTANCE = 0
MAX_DISTANCE = Inf MAX_DISTANCE = Inf
integrate(function(k) pDirectlyPhaseHetPairAndDistanceUsingDepth(meanDepth, nReadsToPhase, L, k, theta, Fm, Fs), lower=MIN_DISTANCE, upper=MAX_DISTANCE, subdivisions=1000)$value iRes = integrate(function(k) pDirectlyPhaseHetPairAndDistanceUsingDepth(meanDepth, nReadsToPhase, L, k, theta, Fm, Fs), lower=MIN_DISTANCE, upper=MAX_DISTANCE, subdivisions=1000, stop.on.error = FALSE)
if (iRes$message != "OK") {
print(paste("DISTANCE INTEGRATION WARNING: ", iRes$message, sep=""))
}
iRes$value
} }
# Probability (over locations of sites on reads, fragment sizes, and read depths) that paired-end reads can TRANSITIVELY phase phaseIndex relative to phaseIndex - 1, given a window of length(windowDistances)+1 het sites at distances given by windowDistances (where an edge in the transitive path requires at least nReadsToPhase reads): # Probability (over locations of sites on reads, fragment sizes, and read depths) that paired-end reads can TRANSITIVELY phase phaseIndex relative to phaseIndex - 1, given a window of length(windowDistances)+1 het sites at distances given by windowDistances (where an edge in the transitive path requires at least nReadsToPhase reads):