Question: (Closed) annotating gene for transcript type/biotype
0
gravatar for sjmonkley
3.8 years ago by
sjmonkley20
Sweden
sjmonkley20 wrote:

I am trying to annotate a table of genes with transcript type (TXTYPE) using Homo.sapiens annotation package within Annotation.Dbi . I want to do this so I can select for only rotein coding genes and remove all the RNA encoding and psuedogenes

I m using the following code:

all_genes$TxType <- mapIds(Homo.sapiens,
                     keys=row.names(all_genes),
                     column="TXTYPE",
                     keytype="SYMBOL",
                     multiVals="first").

However in the Tx.type column is just full of n/a's. The code works with GeneName as column. 

Is the problem that only transcripts rather than genes can be annotated with TXTYPE information?

 

 sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252    LC_MONETARY=Swedish_Sweden.1252
[4] LC_NUMERIC=C                    LC_TIME=Swedish_Sweden.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] dplyr_0.4.3                             Homo.sapiens_1.3.1                     
 [3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 org.Hs.eg.db_3.2.3                     
 [5] GO.db_3.2.2                             RSQLite_1.0.0                          
 [7] DBI_0.3.1                               OrganismDbi_1.12.0                     
 [9] GenomicFeatures_1.22.2                  GenomicRanges_1.22.0                   
[11] GenomeInfoDb_1.6.0                      AnnotationDbi_1.32.0                   
[13] IRanges_2.4.0                           S4Vectors_0.8.0                        
[15] Biobase_2.30.0                          BiocGenerics_0.16.0                    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.1                graph_1.48.0               magrittr_1.5              
 [4] XVector_0.10.0             zlibbioc_1.16.0            GenomicAlignments_1.6.1   
 [7] BiocParallel_1.4.0         R6_2.1.1                   tools_3.2.2               
[10] SummarizedExperiment_1.0.0 lambda.r_1.1.7             futile.logger_1.4.1       
[13] lazyeval_0.1.10            assertthat_0.1             RBGL_1.46.0               
[16] rtracklayer_1.30.1         futile.options_1.0.0       bitops_1.0-6              
[19] RCurl_1.95-4.7             biomaRt_2.26.0             BiocInstaller_1.20.0      
[22] Biostrings_2.38.0          Rsamtools_1.22.0           XML_3.98-1.3   

annotation homo.sapiens • 656 views
ADD COMMENTlink written 3.8 years ago by sjmonkley20

Hello sjmonkley!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 3.8 years ago by James W. MacDonald50k
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