diff --git a/inst/scripts/add_annotation.R b/inst/scripts/add_annotation.R index 1fc190d..611c176 100755 --- a/inst/scripts/add_annotation.R +++ b/inst/scripts/add_annotation.R @@ -34,9 +34,9 @@ option_list <- list( optparse::make_option(c("-o", "--output_file"), type="character", default='Annotated_table.txt', help="Define the output path. Default = %default"), optparse::make_option(c("-c", "--column"), type="character", default=1, - help="Column name or index with ensembl_IDs. Default = %default"), + help="Column name or index or 'rownames' with ensembl_IDs. Default = %default"), optparse::make_option(c("-m", "--mirna"), type= "logical", default = FALSE, action ="store_true", - help= "Indicate if the ids to translate are miRNA (from miRBase to mature ID). If activated, -I and -K are ignored"), + help= "Indicate if the ids to translate are miRNA (from miRBase to mature ID). If activated -O, -I and -K are ignored"), optparse::make_option(c("-I", "--input_keytype"), type="character", default=NULL, help="Set the input keytype. Default=%default : All possible keytypes will be printed"), optparse::make_option(c("-K", "--output_keytype"), type="character", default="SYMBOL",