Hi,
Note sure why but subsetting by name is *very* slow when the character
vector used as subscript contains a lot of "invalid" names:
x <- c(A=10L, B=20L, C=30L)
subscript <- c(LETTERS[1:3], sprintf("ID%05d", 1:150000))
> system.time(y1 <- x[subscript])
user system elapsed
111.991 0.000 112.230
Since subsetting by name is basically equivalent to
i <- match(subscript, names(x))
x[i]
it's quite surprising that the former is more than 10 thousand times
slower than the latter:
> system.time({i <- match(subscript, names(x)); y2 <- x[i]})
user system elapsed
0.008 0.000 0.007
> identical(y2, y1)
[1] TRUE
Thanks,
H.
PS: This issue was already reported here
https://stat.ethz.ch/pipermail/r-devel/2010-July/057945.html
in 2010, and with a proposed fix by Martin Morgan.
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-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] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] GenomicRanges_1.13.8 IRanges_1.19.3 BiocGenerics_0.7.2
loaded via a namespace (and not attached):
[1] stats4_3.0.0 tools_3.0.0
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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