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