comparison cpm_tpm_rpk.R @ 5:bcff1eb6fdb5 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d6ef3d1c1d490967b7b79138573a86a8d5235c43
author artbio
date Fri, 06 Oct 2023 18:00:05 +0000
parents be358a1ebf67
children f00c1c34565e
comparison
equal deleted inserted replaced
4:be358a1ebf67 5:bcff1eb6fdb5
159 return(tpm) 159 return(tpm)
160 } 160 }
161 161
162 #### running code #### 162 #### running code ####
163 163
164 data <- read.table( 164 data <- read.delim(
165 opt$data, 165 opt$data,
166 check.names = FALSE, 166 check.names = FALSE,
167 header = opt$colnames, 167 header = opt$colnames,
168 row.names = 1, 168 row.names = 1,
169 sep = opt$sep 169 sep = opt$sep
170 ) 170 )
171 171
172 if (opt$type == "tpm" || opt$type == "rpk") { 172 if (opt$type == "tpm" || opt$type == "rpk") {
173 gene_length <- as.data.frame( 173 gene_length <- as.data.frame(
174 read.table( 174 read.delim(
175 opt$gene, 175 opt$gene,
176 header = opt$gene_header, 176 header = opt$gene_header,
177 row.names = 1, 177 row.names = 1,
178 sep = opt$gene_sep 178 sep = opt$gene_sep
179 ) 179 )