hello,
I'm currently working on a proteogenomics project, and using customProDB to generate a custom protein database, it's a great R package and i find it really helpful.
Since the last package update i noticed that the function OutputVarproseq has started generating the following error :
Error in `[.data.frame`(snvproseq, , c("pro_name", "peptide", "tx_name.x", :undefined columns selected
after debugging it, i noticed that a new piece of code has been added offering a compatibility with proBAMr which is a very good idea. The following text of code will point to the source of the error :
function OutputVarproseq line 114 :
#######used as input for proBAMr
snvproseq <- ftab
snvproseq[, 'pro_name'] <- paste(snvproseq[, 'pro_name'],
"_", snvproseq[, 'var_name'], sep='')
snvproseq <- snvproseq[, c('pro_name', 'peptide', 'tx_name.x',
'pro_name_v', 'gene_name', 'description')]
### pro_name_v : doesn't exist yet
colnames(snvproseq) <- c('pro_name', 'peptide', 'tx_name', 'pro_name_v',
'gene_name', 'description')
snvproseq
proof :
colnames(ftab) [1] "pro_name" "peptide" "tx_name.x" "var_name" "gene_name" [6] "tx_name.y" "description" snvproseq <- ftab
colnames(snvproseq)
[1] "pro_name" "peptide" "tx_name.x" "var_name" "gene_name"
[6] "tx_name.y" "description"
snvproseq[, 'pro_name'] <- paste(snvproseq[, 'pro_name'], "_", snvproseq[, 'var_name'], sep='')
snvproseq <- snvproseq[, c('pro_name', 'peptide', 'tx_name.x',
'pro_name_v', 'gene_name', 'description')]
## ERROR while selecting pro_name_v column which doesn't exist yet
## must be replaced with :
## snvproseq <- snvproseq[, c('pro_name', 'peptide', 'tx_name.x',
## 'var_name', 'gene_name', 'description')]
colnames(snvproseq) <- c('pro_name', 'peptide', 'tx_name', 'pro_name_v',
'gene_name', 'description')
sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicFeatures_1.26.0 GenomicRanges_1.26.1 GenomeInfoDb_1.10.1
[4] customProDB_1.14.0 biomaRt_2.30.0 AnnotationDbi_1.36.0
[7] Biobase_2.34.0 IRanges_2.8.1 S4Vectors_0.12.1
[10] BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.5 magrittr_1.5
[3] XVector_0.14.0 zlibbioc_1.20.0
[5] GenomicAlignments_1.10.0 BiocParallel_1.8.1
[7] BSgenome_1.42.0 lattice_0.20-33
[9] plyr_1.8.4 stringr_1.0.0
[11] tools_3.3.1 SummarizedExperiment_1.4.0
[13] grid_3.3.1 DBI_0.4-1
[15] Matrix_1.2-6 rtracklayer_1.34.1
[17] bitops_1.0-6 RCurl_1.95-4.8
[19] RSQLite_1.0.0 stringi_1.1.1
[21] Rsamtools_1.26.1 Biostrings_2.42.1
[23] XML_3.98-1.4 VariantAnnotation_1.20.2
please correct me if you have another explanation of how the code works.
Thank you.
