Hi Renaud,
Nice catch! This has been unnoticed for more than 5 years. Should be
fixed in AnnotationDbi release (1.20.7) and devel (1.21.15). Both
versions should become available via biocLite() in the next 24 hours
or so.
Thanks for the report,
H.
On 03/14/2013 06:57 AM, Renaud Gaujoux wrote:
Hi,
I get strange (incorrect?) output from AnnotationDbi::mget when using it on
a subset bimap object with argument ifnotfound=NA.
Keys that exist in the original map are incorrectly returned as found, keys
that don't are correctly returned as NA (See code and output below).
Any idea? Can anybody reproduce this?
Thank you
Renaud
##########################
## code
##########################
library(org.Hs.eg.db)
map <- org.Hs.egUNIGENE
# get some mappedkeys
k <- c(mappedkeys(map)[1:3], 'notakey')
# subset the map using only part of the keys
map2 <- map[k[1:2]]
keys(map2)
# try to get all keys from the subset map:
AnnotationDbi::mget(k, map2) # OK error on third key
AnnotationDbi::mget(k, map2, ifnotfound=NA) # Not OK: the third element
should be NA, right?
sessionInfo()
##############################
####
## output
##################################
R version 2.15.3 (2013-03-01) -- "Security Blanket"
Copyright (C) 2013 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i686-pc-linux-gnu (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
library(org.Hs.eg.db)
Loading required package: AnnotationDbi
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following object(s) are masked from ‘package:stats’:
xtabs
The following object(s) are masked from ‘package:base’:
anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
rownames, sapply, setdiff, table, tapply, union, unique
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DBI
map <- org.Hs.egUNIGENE
# get some mappedkeys
k <- c(mappedkeys(map)[1:3], 'notakey')
# subset the map using only part of the keys
map2 <- map[k[1:2]]
keys(map2)
[1] "1" "10"
# try to get all keys from the subset map:
AnnotationDbi::mget(k, map2) # OK error on third key
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) :
value for "100" not found
AnnotationDbi::mget(k, map2, ifnotfound=NA) # Not OK: the third element
should be NA, right?
$`1`
[1] "Hs.529161" "Hs.709582"
$`10`
[1] "Hs.2"
$`100`
[1] "Hs.654536"
$notakey
[1] NA
sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: i686-pc-linux-gnu (32-bit)
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=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.Hs.eg.db_2.8.0 RSQLite_0.11.2 DBI_0.2-5
[4] AnnotationDbi_1.20.6 Biobase_2.18.0 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] IRanges_1.16.6 parallel_2.15.3 stats4_2.15.3
[[alternative HTML version deleted]]
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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