[BioC] remove NA from named character vector

[axel.klenk at actelion.com]

Hi Iain,

you cannot test for NA using the == operator, you'll have to use is.na(), 
eg.

which(is.na(egs))

or, if you just want to get rid of them:

na.omit(egs)

HTH,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland




From:
Iain Gallagher <iaingallagher at btopenworld.com>
To:
bioconductor <bioconductor at stat.math.ethz.ch>
Date:
22.07.2011 13:03
Subject:
[BioC] remove NA from named character vector
Sent by:
bioconductor-bounces at r-project.org



Hi List

This is likely a trivial problem but it's annoying me. I am mapping from 
Bos taurus ensembl ids to symbols. I can do this in biomaRt but use of the 
org.Bt.eg.db package means I'm not tied to an internet connection. 

A toy example:

library(org.Bt.eg.db)
ens <- c('ENSBTAG00000004218', 'ENSBTAG00000004270', 'ENSBTAG00000004578', 
'ENSBTAG00000004608')
egs <- unlist(mget(ens, revmap(org.Bt.egENSEMBL), ifnotfound=NA))

egs

ENSBTAG00000004218 ENSBTAG00000004270 ENSBTAG00000004578 
ENSBTAG00000004608 
          "617660"           "407106"                 NA "100138951" 

# a named character vector with one NA

#now get symbols
syms <- unlist(mget(egs, org.Bt.egSYMBOL, ifnotfound=NA))

#throws and error - fair enough - need to drop the NA

which(egs == NA)

#gives named integer(0) - hmm
class(egs)
#gives [1] "character" - so I'm quite confused now.

NA %in% egs
#gives [1] TRUE


How do I identify which entries in 'egs' are NA so I can remove them? It's 
trivial here but the dataset I'm working with is in the thousands.

Thanks

iain

> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C 
 [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8 
 [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8 
 [7] LC_PAPER=en_GB.utf8       LC_NAME=C 
 [9] LC_ADDRESS=C              LC_TELEPHONE=C 
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C 

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

other attached packages:
[1] org.Bt.eg.db_2.5.0   RSQLite_0.9-4        DBI_0.2-5 
[4] AnnotationDbi_1.14.1 Biobase_2.10.0 


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