zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Vectorize() pDirectlyPhaseHetPairAtDistanceUsingDepth; deal with minor precision issues 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4890 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2010-12-21 17:18:26 +00:00
parent 09c7ea879d
commit cc909602c7
1 changed files with 16 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

18
R/phasing/RBP_theoretical.R
View File

@ -121,8 +121,18 @@ pFragmentsReadsCanCoverHetPairAtDistance <- function(L, k, Fm, Fs) {
# = Sum_from_d=0^to_d=2*meanDepth { p(having d reads | poisson with meanDepth) * p(there at least nReadsToPhase succeed in phasing x,y | given d reads in total) } # = Sum_from_d=0^to_d=2*meanDepth { p(having d reads | poisson with meanDepth) * p(there at least nReadsToPhase succeed in phasing x,y | given d reads in total) }
# p(having d reads | poisson with meanDepth) = dpois(d, meanDepth) # p(having d reads | poisson with meanDepth) = dpois(d, meanDepth)
# p(there are at least nReadsToPhase that succeed in phasing x,y | given d reads in total) = pbinom(nReadsToPhase - 1, k, pFragmentsReadsCanCoverHetPairAtDistance(L, k, Fm, Fs), lower.tail = FALSE) # p(there are at least nReadsToPhase that succeed in phasing x,y | given d reads in total) = pbinom(nReadsToPhase - 1, k, pFragmentsReadsCanCoverHetPairAtDistance(L, k, Fm, Fs), lower.tail = FALSE)
pDirectlyPhaseHetPairAtDistanceUsingDepth <- function(meanDepth, nReadsToPhase, L, k, Fm, Fs) { pDirectlyPhaseHetPairAtDistanceUsingDepth_SINGLE_k <- function(meanDepth, nReadsToPhase, L, k, Fm, Fs) {
THRESH = 10^-8
p = pFragmentsReadsCanCoverHetPairAtDistance(L, k, Fm, Fs) p = pFragmentsReadsCanCoverHetPairAtDistance(L, k, Fm, Fs)
# deal with numerical issues:
if (abs(1 - p) < THRESH) {
p = 1
}
else if (abs(p) < THRESH) {
p = 0
}
pAtLeastNreadsToPhaseGivenDepth <- function(d) pbinom(nReadsToPhase - 1, d, p, lower.tail = FALSE) pAtLeastNreadsToPhaseGivenDepth <- function(d) pbinom(nReadsToPhase - 1, d, p, lower.tail = FALSE)
pAtLeastNreadsToPhaseAndDepth <- function(d) dpois(d, meanDepth) * pAtLeastNreadsToPhaseGivenDepth(d) pAtLeastNreadsToPhaseAndDepth <- function(d) dpois(d, meanDepth) * pAtLeastNreadsToPhaseGivenDepth(d)
@ -131,8 +141,12 @@ pDirectlyPhaseHetPairAtDistanceUsingDepth <- function(meanDepth, nReadsToPhase,
sum(apply(as.matrix(minDepth:maxDepth), 1, pAtLeastNreadsToPhaseAndDepth)) sum(apply(as.matrix(minDepth:maxDepth), 1, pAtLeastNreadsToPhaseAndDepth))
} }
pDirectlyPhaseHetPairAtDistanceUsingDepth <- function(meanDepth, nReadsToPhase, L, k, Fm, Fs) {
Vectorize(function(dist) pDirectlyPhaseHetPairAtDistanceUsingDepth_SINGLE_k(meanDepth, nReadsToPhase, L, dist, Fm, Fs))(k)
}
pDirectlyPhaseHetPairAndDistanceUsingDepth <- function(meanDepth, nReadsToPhase, L, k, theta, Fm, Fs) { pDirectlyPhaseHetPairAndDistanceUsingDepth <- function(meanDepth, nReadsToPhase, L, k, theta, Fm, Fs) {
Vectorize(function(dist) pDirectlyPhaseHetPairAtDistanceUsingDepth(meanDepth, nReadsToPhase, L, dist, Fm, Fs) * pHetPairAtDistance(dist, theta))(k) pDirectlyPhaseHetPairAtDistanceUsingDepth(meanDepth, nReadsToPhase, L, k, Fm, Fs) * pHetPairAtDistance(k, theta)
} }
# Probability (over locations of x on the read, fragment sizes, read depths, and het-het distances) that that there exist at least nReadsToPhase paired-end reads covering both sites x and y (where the distance between x and y is as per the geometric/exponential distribution): # Probability (over locations of x on the read, fragment sizes, read depths, and het-het distances) that that there exist at least nReadsToPhase paired-end reads covering both sites x and y (where the distance between x and y is as per the geometric/exponential distribution):