From 56be2d2185d74d1ca5f2a8a9668214228750d77f Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Mon, 27 Feb 2023 15:38:12 -0600 Subject: [PATCH] updating DMP.key from fread to read.csv --- R/compile_reads.R | 2 +- R/compile_reads_all.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/compile_reads.R b/R/compile_reads.R index f30735c..ac9833a 100644 --- a/R/compile_reads.R +++ b/R/compile_reads.R @@ -32,7 +32,7 @@ compile_reads <- function( } # data from DMP ----------------------------------------------------------- - DMP.key <- fread(dmp.key.path) + DMP.key <- as.data.table(read.csv(dmp.key.path, header = FALSE, sep = ",")) if (any(!master.ref[grepl("^P-", dmp_patient_id)]$dmp_patient_id %in% gsub("-T..-IH.|-T..-IM.|-T..-XS", "", DMP.key[grepl("IH|IM|XS", V1)]$V1))) { stop(paste0( "These DMP IDs are not found in DMP key file: ", diff --git a/R/compile_reads_all.R b/R/compile_reads_all.R index 364c4b8..d252a82 100644 --- a/R/compile_reads_all.R +++ b/R/compile_reads_all.R @@ -39,7 +39,7 @@ compile_reads_all <- function(master.ref, } # data from DMP ----------------------------------------------------------- - DMP.key <- fread(dmp.key.path) + DMP.key <- as.data.table(read.csv(dmp.key.path, header = FALSE, sep = ",")) if (any(!master.ref[grepl("^P-", dmp_patient_id)]$dmp_patient_id %in% gsub("-T..-IH.|-T..-IM.", "", DMP.key[grepl("IH|IM", V1)]$V1))) { message(paste0( "These DMP IDs are not found in DMP key file: ",