From 8f9dd03e876a93931e48f2ee28ec220a823128c7 Mon Sep 17 00:00:00 2001 From: hanna Date: Tue, 15 Sep 2009 15:53:06 +0000 Subject: [PATCH] Get rid of unnecessary files for generating recalibration data. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1626 348d0f76-0448-11de-a6fe-93d51630548a --- R/logistic_regression.R | 16 ---------------- packages/GenomeAnalysisTK.xml | 3 --- 2 files changed, 19 deletions(-) delete mode 100755 R/logistic_regression.R diff --git a/R/logistic_regression.R b/R/logistic_regression.R deleted file mode 100755 index 604323427..000000000 --- a/R/logistic_regression.R +++ /dev/null @@ -1,16 +0,0 @@ -#!/broad/tools/apps/R-2.6.0/bin/Rscript - -args<- commandArgs(TRUE) -verbose<- TRUE - -input_fileroot <- args[1] -output_fileroot <- args[2] -dinuc <- args[3] - -currentin=paste(input_fileroot,dinuc,"csv",sep="."); -currentout=paste(output_fileroot,dinuc,"parameters",sep="."); -con <- file(currentin, "r") -con_out <- file(currentout, "w+") -data<-read.table(con,header=TRUE,sep=",") -reg<-glm(indicator~1+logitQ+I(logitQ^2)+I(logitQ^3)+I(logitQ^4)+pos+I(logitQ*pos)+I((logitQ^2)*pos)+I((logitQ^3)*pos)+I((logitQ^4)*pos)+I(pos^2)+I(logitQ*(pos^2))+I((logitQ^2)*(pos^2))+I((logitQ^3)*(pos^2))+I((logitQ^4)*(pos^2))+I(pos^3)+I(logitQ*(pos^3))+I((logitQ^2)*(pos^3))+I((logitQ^3)*(pos^3))+I((logitQ^4)*(pos^3))+I(pos^4)+I(logitQ*(pos^4))+I((logitQ^2)*(pos^4))+I((logitQ^3)*(pos^4))+I((logitQ^4)*(pos^4)),family=binomial("logit"),data=data, weights=data$count) -write(coefficients(reg),file=con_out) diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml index eeaad6a18..f93ba0680 100644 --- a/packages/GenomeAnalysisTK.xml +++ b/packages/GenomeAnalysisTK.xml @@ -51,11 +51,8 @@ testdata/exampleFASTA.fasta.fai testdata/exampleFASTA.dict - python/analyzeRecalQuals.py python/analyzeRecalQuals_1KG.py - testdata/defaultGATKConfig.cfg testdata/recalConfig_1KG.cfg - R/logistic_regression.R R/plot_q_emp_stated_hst.R R/plot_qual_diff_v_cycle.R R/plot_qual_diff_v_dinuc.R