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ApobecExp.DataDictionary.cls
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ApobecExp.DataDictionary.cls
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///
/// Class for the reference data
///
Class ApobecExp.DataDictionary [ Abstract ]
{
/// Chromosome names indexed by integer
ClassMethod SetChromosomeNames()
{
kill ^chr
set ^chr(1) = "chr1"
set ^chr(2) = "chr2"
set ^chr(3) = "chr3"
set ^chr(4) = "chr4"
set ^chr(5) = "chr5"
set ^chr(6) = "chr6"
set ^chr(7) = "chr7"
set ^chr(8) = "chr8"
set ^chr(9) = "chr9"
set ^chr(10) = "chr10"
set ^chr(11) = "chr11"
set ^chr(12) = "chr12"
set ^chr(13) = "chr13"
set ^chr(14) = "chr14"
set ^chr(15) = "chr15"
set ^chr(16) = "chr16"
set ^chr(17) = "chr17"
set ^chr(18) = "chr18"
set ^chr(19) = "chr19"
set ^chr(20) = "chr20"
set ^chr(21) = "chr21"
set ^chr(22) = "chr22"
set ^chr(23) = "chrX"
set ^chr(24) = "chrY"
set ^chr = 24
}
/// Chromosome names indexed by lowercase chromosome names
ClassMethod SetChromosomeLowerName()
{
kill ^chrname
set ^chrname("chr1") = "chr1"
set ^chrname("chr2") = "chr2"
set ^chrname("chr3") = "chr3"
set ^chrname("chr4") = "chr4"
set ^chrname("chr5") = "chr5"
set ^chrname("chr6") = "chr6"
set ^chrname("chr7") = "chr7"
set ^chrname("chr8") = "chr8"
set ^chrname("chr9") = "chr9"
set ^chrname("chr10") = "chr10"
set ^chrname("chr11") = "chr11"
set ^chrname("chr12") = "chr12"
set ^chrname("chr13") = "chr13"
set ^chrname("chr14") = "chr14"
set ^chrname("chr15") = "chr15"
set ^chrname("chr16") = "chr16"
set ^chrname("chr17") = "chr17"
set ^chrname("chr18") = "chr18"
set ^chrname("chr19") = "chr19"
set ^chrname("chr20") = "chr20"
set ^chrname("chr21") = "chr21"
set ^chrname("chr22") = "chr22"
set ^chrname("chrx") = "chrX"
set ^chrname("chry") = "chrY"
set ^chr = 24
}
/// Standard abbreviation of the cancer types
ClassMethod SetCancerTypes()
{
kill ^cancerType
set ^cancerType(1) = "BLCA"
set ^cancerType(2) = "BRCA"
set ^cancerType(3) = "HNSC"
set ^cancerType(4) = "LUAD"
set ^cancerType(5) = "LUSC"
set ^cancerType = 5
}
/// Cell lines
ClassMethod SetCellLinesReplication()
{
kill ^cellLinesRT
set ^cellLinesRT(1) = "IMR90"
set ^cellLinesRT(2) = "MCF7"
set ^cellLinesRT(3) = "NHEK"
set ^cellLinesRT = 3
}
/// Correspondense of the cancer types and cell lines
ClassMethod SetCancer2RTCellLines()
{
set ^cancerTypeRTCellLines("BLCA") = "NHEK"
set ^cancerTypeRTCellLines("BRCA") = "MCF7"
set ^cancerTypeRTCellLines("HNSC") = "NHEK"
set ^cancerTypeRTCellLines("LUAD") = "IMR90"
set ^cancerTypeRTCellLines("LUSC") = "IMR90"
}
/// Expression bins bounds in case of 15 bins breakdown
ClassMethod SetExpressionBins14()
{
set ^expBins14(-9999999,0) = 0
set ^expBins14(0,10) = 1
set ^expBins14(10,25) = 2
set ^expBins14(25,50) = 3
set ^expBins14(50,100) = 4
set ^expBins14(100,200) = 5
set ^expBins14(200,300) = 6
set ^expBins14(300,400) = 7
set ^expBins14(400,550) = 8
set ^expBins14(550,700) = 9
set ^expBins14(700,1000) = 10
set ^expBins14(1000,1400) = 11
set ^expBins14(1400,2000) = 12
set ^expBins14(2000,3500) = 13
set ^expBins14(3500,99999999999) = 14
set ^expBins14 = 14
}
/// Expression bins bounds in case of 8 bins breakdown
ClassMethod SetExpressionBins()
{
set ^expBins(-9999999,0) = 0
set ^expBins(0,25) = 1
set ^expBins(25,100) = 2
set ^expBins(100,300) = 3
set ^expBins(300,550) = 4
set ^expBins(550,1000) = 5
set ^expBins(1000,2000) = 6
set ^expBins(2000,99999999999) = 7
set ^expBins = 7
}
}