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mkazanovmkazanov
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Export results class
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‎ApobecExp.ExportData.cls

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///
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/// Class for exporting results of the analysis
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///
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Class ApobecExp.ExportData [ Abstract ]
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{
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/// Prepare results of the APOBEC mutations density
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/// relative replication timing for exporting
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ClassMethod PlotRT()
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{
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kill ^plotRTAPOBEC
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kill ^plotRTOther
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for i = 1:1:^cancerType
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{
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set cancer = ^cancerType(i)
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set cellline = ^cancerTypeRTCellLines(cancer)
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set sample = $order(^mutation(cancer,""))
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while (sample '= "")
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{
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for j = 1:1:7 {
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set ^plotRTAPOBEC(cancer,sample,j) = ^RTresultsAPOBEC(cancer,sample,j)/^RTnumTCW(cellline,j) }
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set total = 0
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for j = 1:1:7 {
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set total = total + ^plotRTAPOBEC(cancer,sample,j) }
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for j = 1:1:7 {
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set ^plotRTAPOBEC(cancer,sample,j) = ^plotRTAPOBEC(cancer,sample,j) / total }
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for j = 1:1:7 {
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set ^plotRTOther(cancer,sample,j) = ^RTresultsOther(cancer,sample,j)/^RTnumAll(cellline,j) }
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set total = 0
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for j = 1:1:7 {
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set total = total + ^plotRTOther(cancer,sample,j) }
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for j = 1:1:7 {
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set ^plotRTOther(cancer,sample,j) = ^plotRTOther(cancer,sample,j) / total }
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write cancer," ",sample,!
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set sample = $order(^mutation(cancer,sample))
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}
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}
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}
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/// Prepare results of the APOBEC mutations density
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/// relative gene expression for exporting
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ClassMethod PlotExp()
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{
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kill ^plotExpAPOBEC
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kill ^plotExpOther
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for i = 1:1:^cancerType
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{
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set cancer = ^cancerType(i)
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set cellline = ^cancerTypeRTCellLines(cancer)
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set sample = $order(^mutation(cancer,""))
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while (sample '= "")
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{
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for j = 0:1:7 {
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set ^plotExpAPOBEC(cancer,sample,j) = ^expResultsAPOBEC(cancer,sample,j)/^expTCW(cancer,sample,j) }
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set total = 0
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for j = 0:1:7 {
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set total = total + ^plotExpAPOBEC(cancer,sample,j) }
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for j = 0:1:7 {
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set ^plotExpAPOBEC(cancer,sample,j) = ^plotExpAPOBEC(cancer,sample,j) / total }
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for j = 0:1:7 {
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set ^plotExpOther(cancer,sample,j) = ^expResultsOther(cancer,sample,j)/^expAll(cancer,sample,j) }
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set total = 0
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for j = 0:1:7 {
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set total = total + ^plotExpOther(cancer,sample,j) }
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for j = 0:1:7 {
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set ^plotExpOther(cancer,sample,j) = ^plotExpOther(cancer,sample,j) / total }
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write cancer," ",sample,!
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set sample = $order(^mutation(cancer,sample))
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}
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}
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}
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/// Prepare results of the APOBEC mutations density
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/// relative replication timing & gene expression for exporting
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ClassMethod PlotExpRT()
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{
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kill ^plotExpRTAPOBEC
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kill ^plotExpRTOther
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for i = 1:1:^cancerType
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{
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set cancer = ^cancerType(i)
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set cellline = ^cancerTypeRTCellLines(cancer)
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set sample = $order(^mutation(cancer,""))
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while (sample '= "")
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{
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write cancer," ",sample,!
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for j = 1:1:7
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{
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for k = 0:1:7
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{
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write "j=",j,", k=",k,!
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write "APOBEC=",^resultsAPOBEC(cancer,sample,j,k),!
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write "TCW=",^expRTTCW(cancer,sample,j,k),!
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if (^resultsAPOBEC(cancer,sample,j,k) = 0) {
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set ^plotExpRTAPOBEC(cancer,sample,j,k) = 0 }
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else {
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set ^plotExpRTAPOBEC(cancer,sample,j,k) = ^resultsAPOBEC(cancer,sample,j,k)/^expRTTCW(cancer,sample,j,k) }
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}
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}
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set total = 0
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for j = 1:1:7
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{
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for k = 0:1:7
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{
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set total = total + ^plotExpRTAPOBEC(cancer,sample,j,k)
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}
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}
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for j = 1:1:7
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{
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for k = 0:1:7
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{
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set ^plotExpRTAPOBEC(cancer,sample,j,k) = ^plotExpRTAPOBEC(cancer,sample,j,k) / total
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}
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}
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for j = 1:1:7
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{
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for k = 0:1:7
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{
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write "j=",j,", k=",k,!
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write "Other=",^resultsOther(cancer,sample,j,k),!
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write "All=",^expRTAll(cancer,sample,j,k),!
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if (^resultsOther(cancer,sample,j,k) = 0) {
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set ^plotExpRTOther(cancer,sample,j,k) = 0 }
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else {
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set ^plotExpRTOther(cancer,sample,j,k) = ^resultsOther(cancer,sample,j,k)/^expRTAll(cancer,sample,j,k) }
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}
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}
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set total = 0
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for j = 1:1:7
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{
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for k = 0:1:7
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{
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set total = total + ^plotExpRTOther(cancer,sample,j,k)
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}
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}
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for j = 1:1:7
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{
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for k = 0:1:7
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{
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set ^plotExpRTOther(cancer,sample,j,k) = ^plotExpRTOther(cancer,sample,j,k) / total
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}
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}
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set sample = $order(^mutation(cancer,sample))
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}
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}
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}
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/// Export results of replication timing &
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/// gene epression analysis
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ClassMethod ExportPlotExpRT(dirname As %String = "/home/mkazanov/ApobecExpResults/")
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{
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do $system.Process.SetZEOF(1)
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set filename = dirname_"expRTAPOBEC.txt"
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open filename:"WNS"
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use filename
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write "CANCER_TYPE"_$c(9)_"SAMPLE"_$c(9)_"RT_BIN"_$c(9)_"EXP_BIN"_$c(9)_"MUT_DENSITY",!
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for i = 1:1:^cancerType
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{
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set cancer = ^cancerType(i)
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set sample = $order(^mutation(cancer,""))
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while (sample '= "")
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{
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for j = 1:1:7
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{
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for k = 0:1:7
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{
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write cancer_$c(9)_sample_$c(9)_j_$c(9)_k_$c(9)_^plotExpRTAPOBEC(cancer,sample,j,k),!
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}
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}
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set sample = $order(^mutation(cancer,sample))
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}
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}
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close filename
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set filename = dirname_"expRTOther.txt"
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open filename:"WNS"
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use filename
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write "CANCER_TYPE"_$c(9)_"SAMPLE"_$c(9)_"RT_BIN"_$c(9)_"EXP_BIN"_$c(9)_"MUT_DENSITY",!
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for i = 1:1:^cancerType
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{
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set cancer = ^cancerType(i)
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set sample = $order(^mutation(cancer,""))
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while (sample '= "")
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{
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for j = 1:1:7
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{
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for k = 0:1:7
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{
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write cancer_$c(9)_sample_$c(9)_j_$c(9)_k_$c(9)_^plotExpRTOther(cancer,sample,j,k),!
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}
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}
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set sample = $order(^mutation(cancer,sample))
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}
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}
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close filename
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}
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/// Export results of replication
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/// timing analysis
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ClassMethod ExportPlotRT(dirname As %String = "/home/mkazanov/ApobecExpResults/")
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{
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do $system.Process.SetZEOF(1)
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set filename = dirname_"RTAPOBEC.txt"
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open filename:"WNS"
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use filename
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write "CANCER_TYPE"_$c(9)_"SAMPLE"_$c(9)_"RT_BIN"_$c(9)_"MUT_DENSITY",!
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for i = 1:1:^cancerType
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{
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set cancer = ^cancerType(i)
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set sample = $order(^mutation(cancer,""))
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while (sample '= "")
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{
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for j = 1:1:7
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{
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write cancer_$c(9)_sample_$c(9)_j_$c(9)_^plotRTAPOBEC(cancer,sample,j),!
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}
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set sample = $order(^mutation(cancer,sample))
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}
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}
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close filename
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set filename = dirname_"RTOther.txt"
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open filename:"WNS"
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use filename
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write "CANCER_TYPE"_$c(9)_"SAMPLE"_$c(9)_"RT_BIN"_$c(9)_"MUT_DENSITY",!
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for i = 1:1:^cancerType
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{
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set cancer = ^cancerType(i)
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set sample = $order(^mutation(cancer,""))
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while (sample '= "")
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{
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for j = 1:1:7
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{
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write cancer_$c(9)_sample_$c(9)_j_$c(9)_^plotRTOther(cancer,sample,j),!
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}
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set sample = $order(^mutation(cancer,sample))
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}
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}
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close filename
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}
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/// Export results of gene
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/// expression analysis
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ClassMethod ExportPlotExp(dirname As %String = "/home/mkazanov/ApobecExpResults/")
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{
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do $system.Process.SetZEOF(1)
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set filename = dirname_"expAPOBEC.txt"
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open filename:"WNS"
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use filename
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write "CANCER_TYPE"_$c(9)_"SAMPLE"_$c(9)_"EXP_BIN"_$c(9)_"MUT_DENSITY",!
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for i = 1:1:^cancerType
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{
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set cancer = ^cancerType(i)
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set sample = $order(^mutation(cancer,""))
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while (sample '= "")
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{
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for j = 0:1:7
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{
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write cancer_$c(9)_sample_$c(9)_j_$c(9)_^plotExpAPOBEC(cancer,sample,j),!
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}
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set sample = $order(^mutation(cancer,sample))
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}
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}
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close filename
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set filename = dirname_"expOther.txt"
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open filename:"WNS"
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use filename
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write "CANCER_TYPE"_$c(9)_"SAMPLE"_$c(9)_"EXP_BIN"_$c(9)_"MUT_DENSITY",!
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for i = 1:1:^cancerType
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{
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set cancer = ^cancerType(i)
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set sample = $order(^mutation(cancer,""))
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while (sample '= "")
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{
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for j = 0:1:7
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{
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write cancer_$c(9)_sample_$c(9)_j_$c(9)_^plotExpOther(cancer,sample,j),!
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}
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set sample = $order(^mutation(cancer,sample))
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}
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}
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close filename
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}
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/// Export APOBEC enrichment data
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///
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ClassMethod ExportEnrichment(dirname As %String = "/home/mkazanov/ApobecExpResults/")
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{
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set filename = dirname_"sample_enrichent.txt"
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open filename:"WNS"
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use filename
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write "CANCER_TYPE"_$c(9)_"SAMPLE"_$c(9)_"APOBEC_ENRICHMENT",!
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for i = 1:1:^cancerType
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{
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set cancer = ^cancerType(i)
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set sample = $order(^sample(cancer,""))
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while (sample '= "")
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{
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set enrich = $listget(^sample(cancer,sample),1)
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write cancer_$c(9)_sample_$c(9)_enrich,!
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set sample = $order(^mutation(cancer,sample))
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}
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}
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close filename
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}
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}

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