From 0a7137616c6cddaa39cac62f71fc276dcdef36f7 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 2 Mar 2012 09:11:59 -0500 Subject: [PATCH] Now converts gatkreports to properly typed R data types in gsa.read.gatkreport -- use the general function type.convert from read.table to automagically convert the string data to booleans, factors, and numeric types as appropriate. Vastly better than the previous behavior which only worked for numerics, in some cases. --- .../sting/utils/R/gsalib/R/gsa.read.gatkreport.R | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R b/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R index 46bbf7eda..876cf5cbc 100644 --- a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R +++ b/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R @@ -4,11 +4,9 @@ colnames(d) = tableHeader; for (i in 1:ncol(d)) { - v = suppressWarnings(as.numeric(d[,i])); - - if (length(na.omit(as.numeric(v))) == length(d[,i])) { - d[,i] = v; - } + # use the general type.convert infrastructure of read.table to convert column data to R types + v = type.convert(d[,i]) + d[,i] = v; } usedNames = ls(envir=tableEnv, pattern=tableName);