Mercurial > repos > peter-waltman > ucsc_cluster_tools2
comparison cluster.tools/extract.TCGA.survival.data.R @ 3:563832f48c08 draft
Uploaded
| author | peter-waltman |
|---|---|
| date | Fri, 01 Mar 2013 19:51:25 -0500 |
| parents | dddfeedb85af |
| children |
comparison
equal
deleted
inserted
replaced
| 2:b8f262149ee2 | 3:563832f48c08 |
|---|---|
| 91 stop( "can't find a valid entry with status info - have tried vital_status & days_to_death\n" ) | 91 stop( "can't find a valid entry with status info - have tried vital_status & days_to_death\n" ) |
| 92 } | 92 } |
| 93 } | 93 } |
| 94 clinical.data <- as.numeric( ! grepl( "(LIVING|Not)", clinical.data ) ) | 94 clinical.data <- as.numeric( ! grepl( "(LIVING|Not)", clinical.data ) ) |
| 95 } | 95 } |
| 96 | |
| 96 if ( is.null(opt$time.column ) ) { | 97 if ( is.null(opt$time.column ) ) { |
| 97 time.colname <- "CDE.clinical_time" | 98 time.colname <- "CDE.clinical_time" |
| 98 | 99 |
| 99 if ( time.colname %in% colnames( orig.clinical.data ) ) { | 100 if ( time.colname %in% colnames( orig.clinical.data ) ) { |
| 100 opt$time.column <- which( colnames( orig.clinical.data ) %in% time.colname ) | 101 opt$time.column <- which( colnames( orig.clinical.data ) %in% time.colname ) |