Entering edit mode
Shi, Tao
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720
@shi-tao-199
Last seen 9.6 years ago
Hi list,
This only happened after I switched to R-2.8.0 and the latest biomaRt
and RCurl. I was using R-2.7.0 before and everything worked fine.
Currently, manually loading RCurl after loading biomaRt solves the
problem. Please see the R outputs below. Many thanks!
##==============================================================
R version 2.8.0 (2008-10-20)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
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(biomaRt)
> ?getSNP
> mart <- useMart("snp",dataset="hsapiens_snp")
Error in curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
:
could not find function "findHTTPHeaderEncoding"
>
> snp = getSNP(chromosome = 8, start = 148350, end = 148612, mart =
mart)
Error in martCheck(mart, "snp") : object "mart" not found
In addition: Warning message:
The getSNP function will be removed in the next release of biomaRt.
Use the getBM function instead. The biomaRt vignette contains
examples of retrieving SNP data
> show(snp)
Error: object "snp" not found
Error in show(snp) :
error in evaluating the argument 'object' in selecting a method for
function 'show'
> ?findHTTPHeaderEncoding
No documentation for 'findHTTPHeaderEncoding' in specified packages
and libraries:
you could try '??findHTTPHeaderEncoding'
> library(RCurl)
> mart <- useMart("snp",dataset="hsapiens_snp")
Checking attributes and filters ... ok
> snp = getSNP(chromosome = 8, start = 148350, end = 148612, mart =
mart)
Warning message:
The getSNP function will be removed in the next release of biomaRt.
Use the getBM function instead. The biomaRt vignette contains
examples of retrieving SNP data
> snp
refsnp_id allele chrom_start chrom_strand
1 rs13291 C/T 148462 1
2 rs1134186 T/C 148569 1
3 rs1134187 G/A 148539 -1
4 rs1134189 G/A 148535 -1
5 rs1134190 C/T 148533 -1
6 rs1134191 C/T 148499 -1
7 rs1134192 G/A 148462 -1
8 rs1134195 G/T 148394 -1
9 rs3965587 C/T 148535 1
10 rs4046274 C/A 148394 1
11 rs4046275 A/G 148411 1
12 rs4046276 C/T 148462 1
13 rs4046277 G/A 148499 1
14 rs4046278 G/A 148533 1
15 rs4378731 G/A 148601 1
16 rs11136408 G/A 148525 1
17 rs12019378 T/G 148471 1
> sessionInfo()
R version 2.8.0 (2008-10-20)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RCurl_0.9-4 biomaRt_1.16.0
loaded via a namespace (and not attached):
[1] XML_1.96-0
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