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summarizeTests.R
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summarizeTests.R
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source("plot-results.R")
load("tcgaResult.RData")
surrogateTable <- read.delim("surrogate-table.txt")
testVec <- c("BT20-BRCA1" , "BT20-BRF1" , "BT20-CASP2" , "BT20-CASP3",
"BT474-BRCA1", "BT474-BRF1", "BT474-CASP2", "BT474-CASP3",
"BT483-BRCA1", "BT483-BRF1", "BT483-CASP2", "BT483-CASP3" ,"BT549-BRCA1", "BT549-BRF1" ,
"BT549-CASP2", "BT549-CASP3")
testVec <- c("HCC1395-APLP2","HCC1395-APPL","HCC1395-AR","HCC1395-ATN1","HCC1395-ATP2B2","HCC1428-APLP2",
"HCC1428-APPL", "HCC1428-AR","HCC1428-ATN1", "HCC1428-ATP2B2", "HCC1569-APLP2", "HCC1569-APPL",
"HCC1569-AR", "HCC1569-ATN1", "HCC1569-ATP2B2", "HCC1806-APLP2", "HCC1806-APPL", "HCC1806-AR",
"HCC1806-ATN1", "HCC1806-ATP2B2", "HCC1937-APLP2", "HCC1937-APPL", "HCC1937-AR", "HCC1937-ATN1",
"HCC1937-ATP2B2", "HCC1954-APLP2", "HCC1954-APPL", "HCC1954-AR", "HCC1954-ATN1", "HCC1954-ATP2B2",
"HCC202-APLP2", "HCC202-APPL", "HCC202-AR", "HCC202-ATN1", "HCC202-ATP2B2" )
summarizeNetworks(testVec, intome, tcgaResult$mutCopyFrames,
surrogateTable, geneIntTable, NULL)
testVec <- as.character(surrogateTable[surrogateTable$Gene == "ESR1","ID"])
testVec <- as.character(surrogateTable[surrogateTable$Gene == "BRCA1","ID"])
testVec <- as.character(surrogateTable[surrogateTable$Gene == "RB1","ID"])
testVec <- as.character(surrogateTable[surrogateTable$Gene == "MAPK9","ID"])
testVec <- as.character(surrogateTable[surrogateTable$Gene == "SMARCB1","ID"])
testVec <- as.character(surrogateTable[surrogateTable$Gene == "PTK2","ID"])
testVec <- as.character(surrogateTable[surrogateTable$Gene == "GSK3B","ID"])
testVec <- as.character(surrogateTable[surrogateTable$Gene == "AR","ID"])
testVec <- as.character(surrogateTable[surrogateTable$Gene == "UBB","ID"])
testVec <- as.character(surrogateTable[surrogateTable$Gene == "CTNNB1","ID"])
testVec <- as.character(surrogateTable[surrogateTable$Sample == "SKBR3" & surrogateTable$pvalue < 0.05,"ID"])
testVec <- as.character(surrogateTable[surrogateTable$Sample == "HCC202" & surrogateTable$pvalue < 0.05,"ID"])
testVec <- as.character(surrogateTable[surrogateTable$Sample == "BT20" & surrogateTable$pvalue < 0.01,"ID"])
summarizeNetworks(testVec, intome, tcgaResult$mutCopyFrames, surrogateTable, geneIntTable, NULL)