Question: customProDB, OutputVarproseq function update (snvproseq)
0
gravatar for georges.bedran
2.5 years ago by
georges.bedran0 wrote:

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.

customprodb • 467 views
ADD COMMENTlink modified 2.5 years ago by xiaojing.wang50 • written 2.5 years ago by georges.bedran0
Answer: customProDB, OutputVarproseq function update (snvproseq)
0
gravatar for xiaojing.wang
2.5 years ago by
United States
xiaojing.wang50 wrote:
Thanks. I'll make some changes of several functions in a few days. Xiaojing From: georges.bedran [bioc] [mailto:noreply@bioconductor.org] Sent: Wednesday, December 07, 2016 7:52 AM To: Wang, Xiaojing <xiaojing.wang@vanderbilt.edu> Subject: [bioc] OutputVarproseq function update (snvproseq) ***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe. ________________________________ Activity on a post you are following on support.bioconductor.org<https: urldefense.proofpoint.com="" v2="" url?u="&lt;a href=" http:="" <a="" href="http://https-3A__support.bioconductor.org" rel="nofollow">https-3A__support.bioconductor.org"="" rel="nofollow">https-3A__support.bioconductor.org&d=DgMFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=kFeMVXg6IR9yZ8yAlLZxpA&m=czNmMiHcHGBuQ7cVA0x2E0v4EpL7kJXQQ5PvjZ8QnNY&s=X7rLokr9y4goWAowzp9NUKdGP0ztlzwb4t2s9qJyrEQ&e="> User georges.bedran<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_u_11010_&amp;d=DgMFAw&amp;c=ZQs-KZ8oxEw0p81sqgiaRA&amp;r=kFeMVXg6IR9yZ8yAlLZxpA&amp;m=czNmMiHcHGBuQ7cVA0x2E0v4EpL7kJXQQ5PvjZ8QnNY&amp;s=z1nQ_x-sdUQW6CSzNbAerCFWKiUe60M-q6kBj4recAU&amp;e="> wrote Question: OutputVarproseq function update (snvproseq)<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_p_90095_&amp;d=DgMFAw&amp;c=ZQs-KZ8oxEw0p81sqgiaRA&amp;r=kFeMVXg6IR9yZ8yAlLZxpA&amp;m=czNmMiHcHGBuQ7cVA0x2E0v4EpL7kJXQQ5PvjZ8QnNY&amp;s=yWp33PlVk6ymhntN4CGofwZMdspPJSbuSKG2eY51rfY&amp;e=">: 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. ________________________________ Post tags: customprodb You may reply via email or visit customProDB, OutputVarproseq function update (snvproseq)
ADD COMMENTlink written 2.5 years ago by xiaojing.wang50
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