Mercurial > repos > shians > shrnaseq
comparison hairpinTool.R @ 4:f8af57d6f60b
Fixed bug causing fastq input to break
- Moved misplaced error check causing fastq inputs to not function
| author | shian_su <registertonysu@gmail.com> |
|---|---|
| date | Mon, 24 Feb 2014 14:41:39 +1100 |
| parents | 076ca575208f |
| children | 3d04308a99f9 |
comparison
equal
deleted
inserted
replaced
| 2:076ca575208f | 4:f8af57d6f60b |
|---|---|
| 168 offenders <- unmake.names(offenders) | 168 offenders <- unmake.names(offenders) |
| 169 stop("ID column of sample annotation must have unique values, values ", | 169 stop("ID column of sample annotation must have unique values, values ", |
| 170 offenders, " are repeated") | 170 offenders, " are repeated") |
| 171 } # Check that IDs in sample annotation are unique | 171 } # Check that IDs in sample annotation are unique |
| 172 | 172 |
| 173 if (any(is.na(match(samples$ID, colnames(counts))))) { | |
| 174 stop("not all samples have groups specified") | |
| 175 } # Check that a group has be specifed for each sample | |
| 176 | |
| 177 if (inputType=="fastq") { | 173 if (inputType=="fastq") { |
| 178 | 174 |
| 179 if (any(table(hairpins$ID)>1)){ | 175 if (any(table(hairpins$ID)>1)){ |
| 180 tab <- table(hairpins$ID) | 176 tab <- table(hairpins$ID) |
| 181 offenders <- paste(names(tab[tab>1]), collapse=", ") | 177 offenders <- paste(names(tab[tab>1]), collapse=", ") |
| 182 stop("ID column of hairpin annotation must have unique values, values ", | 178 stop("ID column of hairpin annotation must have unique values, values ", |
| 183 offenders, " are repeated") | 179 offenders, " are repeated") |
| 184 } # Check that IDs in hairpin annotation are unique | 180 } # Check that IDs in hairpin annotation are unique |
| 185 | 181 |
| 186 } else if (inputType=="counts") { | 182 } else if (inputType=="counts") { |
| 183 if (any(is.na(match(samples$ID, colnames(counts))))) { | |
| 184 stop("not all samples have groups specified") | |
| 185 } # Check that a group has be specifed for each sample | |
| 187 | 186 |
| 188 if (any(table(counts$ID)>1)){ | 187 if (any(table(counts$ID)>1)){ |
| 189 tab <- table(counts$ID) | 188 tab <- table(counts$ID) |
| 190 offenders <- paste(names(tab[tab>1]), collapse=", ") | 189 offenders <- paste(names(tab[tab>1]), collapse=", ") |
| 191 stop("ID column of count table must have unique values, values ", | 190 stop("ID column of count table must have unique values, values ", |
| 291 hpReadout <- gsub(" -- ", "", hpReadout, fixed=TRUE) | 290 hpReadout <- gsub(" -- ", "", hpReadout, fixed=TRUE) |
| 292 | 291 |
| 293 | 292 |
| 294 # Make the names of groups syntactically valid (replace spaces with periods) | 293 # Make the names of groups syntactically valid (replace spaces with periods) |
| 295 data$samples$group <- make.names(data$samples$group) | 294 data$samples$group <- make.names(data$samples$group) |
| 296 } else { | 295 } else if (inputType=="counts") { |
| 297 # Process counts information, set ID column to be row names | 296 # Process counts information, set ID column to be row names |
| 298 rownames(counts) <- counts$ID | 297 rownames(counts) <- counts$ID |
| 299 counts <- counts[ , !(colnames(counts)=="ID")] | 298 counts <- counts[ , !(colnames(counts)=="ID")] |
| 300 countsRows <- nrow(counts) | 299 countsRows <- nrow(counts) |
| 301 | 300 |