From a5e1854b3a6289ab6d33c25cd5d3c423c029a5e2 Mon Sep 17 00:00:00 2001 From: fromer Date: Thu, 16 Dec 2010 01:58:06 +0000 Subject: [PATCH] Forgot to pass correct parameters to calcPhasingProbsForWindowDistances() git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4851 348d0f76-0448-11de-a6fe-93d51630548a --- R/phasing/calcPhasingProbsForWindowDistances.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/phasing/calcPhasingProbsForWindowDistances.R b/R/phasing/calcPhasingProbsForWindowDistances.R index 2de4dbc30..ed6af4ae3 100644 --- a/R/phasing/calcPhasingProbsForWindowDistances.R +++ b/R/phasing/calcPhasingProbsForWindowDistances.R @@ -1,4 +1,4 @@ -calcPhasingProbsForWindowDistances <- function(distances, MAX_WINDOW_SIZE, FILE_NAME = NULL) { +calcPhasingProbsForWindowDistances <- function(distances, MAX_WINDOW_SIZE, meanDepth, nReadsToPhase, L, Fm, Fs, FILE_NAME = NULL) { WINDOW_SIZES = 2:MAX_WINDOW_SIZE phaseProbsPositionWindow = matrix(data = NA, nrow=length(distances), ncol=length(WINDOW_SIZES)) @@ -33,7 +33,7 @@ calcPhasingProbsForWindowDistances <- function(distances, MAX_WINDOW_SIZE, FILE_ windowDistances = distances[useDistancesRange] print(paste("Try to phase position ", i+1, " [relative to ", i, "] using positions: (", paste(usePositionRange, collapse=", "), "), windowDistances= (", paste(windowDistances, collapse=", "), "), [phaseIndex= ", phaseIndex, ", i=", i, "]", sep="")) - p = pPhaseHetPairAtDistanceUsingDepthAndWindow(windowDistances, phaseIndex, meanDepth, nReadsToPhase, L, Im, Is) + p = pPhaseHetPairAtDistanceUsingDepthAndWindow(windowDistances, phaseIndex, meanDepth, nReadsToPhase, L, Fm, Fs) print(paste("phase prob: ", p, sep="")) phaseProbsPositionWindow[i, j] = p }