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drop unnecessary data columns from phenotype dataframe..

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1 parent 4c01011 commit 72506106ccf39a003d7e248d19044ed9ab35d930 @isaak isaak committed Aug 1, 2012
Showing with 3 additions and 12 deletions.
  1. +3 −12 R/gs.r
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15 R/gs.r
@@ -14,10 +14,6 @@ inFile <- grep("input_files",
perl = TRUE,
value = TRUE
)
-print("input files start reading")
-print(inFile)
-
-
outFile <- grep("output_files",
allArgs,
@@ -81,19 +77,14 @@ phenoData <- read.table(phenoFile,
dec = "."
)
-phenoData <- data.matrix(phenoData[order(row.names(phenoData)), ])
+phenoData <- phenoData[order(row.names(phenoData)), ]
-#dropColumns <- c("uniquename", "stock_id")
-#phenoData <- phenoData[,!(names(phenoData) %in% dropColumns)]
-#print("dropped fields")
-print(phenoData)
+dropColumns <- c("uniquename", "stock_id")
+phenoData <- phenoData[,!(names(phenoData) %in% dropColumns)]
phenoTrait <- subset(phenoData,
select = c(trait)
)
-print("select pheno trait")
-print(phenoTrait)
-#phenoData <- phenoTrait
genoFile <- grep("geno",
inFiles,

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