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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
This commit is contained in:
hanna 2009-09-15 15:53:06 +00:00
parent e6827424b9
commit 8f9dd03e87
2 changed files with 0 additions and 19 deletions
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16
R/logistic_regression.R
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@ -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)

3
packages/GenomeAnalysisTK.xml
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@ -51,11 +51,8 @@
<file>testdata/exampleFASTA.fasta.fai</file>
<file>testdata/exampleFASTA.dict</file>
<!-- Supplemental scripts for graph generation, etc. -->
<file>python/analyzeRecalQuals.py</file>
<file>python/analyzeRecalQuals_1KG.py</file>
<file>testdata/defaultGATKConfig.cfg</file>
<file>testdata/recalConfig_1KG.cfg</file>
<file>R/logistic_regression.R</file>
<file>R/plot_q_emp_stated_hst.R</file>
<file>R/plot_qual_diff_v_cycle.R</file>
<file>R/plot_qual_diff_v_dinuc.R</file>