From 47b4881b76af0720ea2ca1a9292e2536d0c9c2e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Wiktor=20Ku=C5=9Bmirek?= Date: Wed, 13 Sep 2017 16:45:47 +0200 Subject: [PATCH 1/2] bugfix in evaluator module (strtoi function) --- R/CNVCALLER.EVALUATOR/R/functions_CNVCALLER.EVALUATOR.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/CNVCALLER.EVALUATOR/R/functions_CNVCALLER.EVALUATOR.R b/R/CNVCALLER.EVALUATOR/R/functions_CNVCALLER.EVALUATOR.R index ba191c3..086ae4e 100644 --- a/R/CNVCALLER.EVALUATOR/R/functions_CNVCALLER.EVALUATOR.R +++ b/R/CNVCALLER.EVALUATOR/R/functions_CNVCALLER.EVALUATOR.R @@ -11,8 +11,8 @@ build_intersection_matrix <- function(calls, refs){ calls[i,"ed_bp"], refs[j,"st_bp"], refs[j,"ed_bp"]) - call_length <- calls[i,"ed_bp"] - calls[i,"st_bp"] - ref_length <- refs[j,"ed_bp"] - refs[j,"st_bp"] + call_length <- strtoi(calls[i,"ed_bp"]) - strtoi(calls[i,"st_bp"]) + ref_length <- strtoi(refs[j,"ed_bp"]) - strtoi(refs[j,"st_bp"]) overlap_factor <- overlap_length / ((call_length + ref_length) / 2) * 100 intersection_matrix[i,j] <- round(overlap_factor, 2) } @@ -77,7 +77,7 @@ calc_cnv_frequency <- function(cnv, calls){ } calc_overlap_length <- function(min1, max1, min2, max2){ - overlap_length <- max(0, min(max1, max2) - max(min1, min2)) + overlap_length <- max(0, min(strtoi(max1), strtoi(max2)) - max(strtoi(min1), strtoi(min2))) overlap_length } From fefa65c2d0916ffad0b539736a665f934d4d448d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Wiktor=20Ku=C5=9Bmirek?= Date: Wed, 13 Sep 2017 16:55:26 +0200 Subject: [PATCH 2/2] missing library --- R/CNVCALLER.EVALUATOR/inst/evaluate_cnvcaller.R | 1 + 1 file changed, 1 insertion(+) diff --git a/R/CNVCALLER.EVALUATOR/inst/evaluate_cnvcaller.R b/R/CNVCALLER.EVALUATOR/inst/evaluate_cnvcaller.R index 24be88e..e78067b 100755 --- a/R/CNVCALLER.EVALUATOR/inst/evaluate_cnvcaller.R +++ b/R/CNVCALLER.EVALUATOR/inst/evaluate_cnvcaller.R @@ -4,6 +4,7 @@ library(devtools) library('CNVCALLER.EVALUATOR') library(optparse) library(RJDBC) +library(stringr) option_list <- list( make_option("--paramsTabName", default="public.evaluation_parameters",