[BioC] gwSnpTests in GGtools
francesca casalino
francy.casalino at gmail.com
Tue Nov 29 16:04:53 CET 2011
Thank you so much for all your valuable information and help.
The gwSnpTests now works, since I specified a function as you suggested:
f1 = gwSnpTests(probeId("10023813203")~GENDER, ss)
However I still find myself having to limit the chromosome data at the
plink import stage to chromosome 19, and can't seem to be able to do
this after the creation of the smlSet. As you say, the gwSnpTeststakes
uses all the SNPs in the smList(smlSet) to run the association, but I
am not getting a list organized by chromosome, and I think my problem
is the original sml_Set list, which I created doing this:
ss<- make_smlSet(es, list("1"=snp.matrix$genotypes))
While I have SNPs from all chromosomes in the snp.matrix$genotypes, I
guess I am indicating wrongly here that I only have one chromosome. Is
it possible to create an smlSet with all the chromosomes, and then
select only some using:
chr19_20 <- getSS("GGtools", c("19", "20"))
Also when I try to find the genesymbol APOE (which is present in the
original plink files) I get:
f2 = gwSnpTests(genesym("APOE")~GENDER, ss)
character(0)
Failed with error: ‘'package' must be of length 1’
Error in revmap(get(paste(gsub(".db", "", annpack), "SYMBOL", sep = ""))) :
error in evaluating the argument 'x' in selecting a method for
function 'revmap': Error in get(paste(gsub(".db", "", annpack),
"SYMBOL", sep = "")) :
object 'SYMBOL' not found
Which could still be due to creating an incorrect sml_Set.
Thank you once more for your all your advices!
-f
2011/11/29 Vincent Carey <stvjc at channing.harvard.edu>:
>
>
> On Tue, Nov 29, 2011 at 5:20 AM, francy [guest] <guest at bioconductor.org>
> wrote:
>>
>>
>> Hi all,
>>
>> I am trying to find eQTLs in or around a particular gene with probe ID=
>> "10023813203" (gene is APOE). I have first selected the SNPs on only my
>> chromosome of interest (chr19), then imported the plink files only for this
>> chromosome doing this:
>>
>> snp.matrix<-read.plink("plink.bed", "plink.bim",
>> "plink.fam",select.snps=chr19)
>>
>> I was able to create an expression set (called 'es'), and a sml_Set by
>> doing this:
>>
>> ss<- make_smlSet(es, list("1"=snp.matrix$genotypes))
>>
>> but I can't seem to go beyond and use this sml_Set to perform the
>> association.
>>
>> When I try this or other combinations of this (e.g. using 'APOE')
>> f1 = gwSnpTests(probeId("10023813203"), ss)
>>
>> Error in function (classes, fdef, mtable) :
>> unable to find an inherited method for function "gwSnpTests", for
>> signature "character", "smlSet", "missing", "missing"
>>
>
> When you encounter an error of this sort, please check what signatures are
> supported:
>
>> showMethods("gwSnpTests")
> Function: gwSnpTests (package GGtools)
> sym="formula", sms="smlSet", cnum="cnumOrMissing", cs="missing"
> sym="formula", sms="smlSet", cnum="snpdepth", cs="missing"
>
> This shows that the first argument should be a formula, and suggests that
> you can have only two arguments if you like.
>
> If you change your call to
>
> f1 = gwSnpTests(probeId("10023813203")~1, ss)
>
> I would expect it to succeed. Note the example code, from R 2.14, which you
> really should be using at this time:
>
>> hmceuB36.2021 <- getSS("GGtools", c("20", "21")) # construct smlSet
>> from prepackaged data
>> hmFou = hmceuB36.2021[, which(hmceuB36.2021$isFounder)] # filter samples
>> to 'founders'
>> f1 = gwSnpTests(genesym("CPNE1")~male, hmFou, chrnum(20)) # execute
>> simple set of tests
>> f1 # there are 119921 tests, so have a concise report
> gwSnpScreenResult for gene CPNE1 [probe GI_23397697-A ]
>> topSnps(f1) # get top results
> p.val
> rs17093026 3.735759e-10
> rs1118233 1.272958e-09
> rs12480408 1.360682e-09
> rs6060535 1.360682e-09
> rs11696527 1.360682e-09
> rs6058303 1.360682e-09
> rs6060578 1.360682e-09
> rs2425078 1.360682e-09
> rs1970357 1.360682e-09
> rs7273815 1.806197e-09
>
>
>
>
>>
>> My first question is, why is the 'gwSnpTests' not working?
>
>
> Please use a supported call sequence.
>
>>
>> My second question is, do I have to select the chromosome I am interested
>> in before creating the sml test? I would have liked to select chromosome 19
>> after so that I could analyse more than this one chromosome if I wanted
>> to…Is this possible?? It seems as the snp.matrix must be in the form of a
>> list, so maybe I have to create a list of all the chromosomes?
>>
>> THANK YOU VERY VERY MUCH FOR ANY HELP YOU COULD GIVE ME!! I really
>> appreciate it!
>>
>
> The signatures show that you can omit the chromosome if you wish. In this
> case,
>
>> f2 = gwSnpTests(genesym("CPNE1")~male, hmFou)
>> f2
> gwSnpScreenResult for gene CPNE1 [probe GI_23397697-A ]
>> topSnps(f2)
> $`20`
> p.val
> rs17093026 3.735759e-10
> rs1118233 1.272958e-09
> rs12480408 1.360682e-09
> rs6060535 1.360682e-09
> rs11696527 1.360682e-09
> rs6058303 1.360682e-09
> rs6060578 1.360682e-09
> rs2425078 1.360682e-09
> rs1970357 1.360682e-09
> rs7273815 1.806197e-09
>
> $`21`
> p.val
> rs2823672 3.024310e-05
> rs4257464 4.340207e-05
> rs16994832 4.340207e-05
> rs2823676 4.340207e-05
> rs2823677 4.340207e-05
> rs8131686 4.340207e-05
> rs2823683 4.340207e-05
> rs238983 4.340207e-05
> rs2828436 4.340207e-05
> rs2828438 4.340207e-05
>
> gwSnpTests will operate on all the SNPs in the smList(smlSet) and return
> lists organized by
> chromosome. Hence the "gw" -- it is possible to compute a genome-wide
> search for eQTL if the
> smlSet contains SNP from all chromosomes. A few years ago this was quite
> reasonable when we
> handled, say, 4 million SNP. Then it became less reasonable when we started
> to work with 8 million
> SNP. So the infrastructure changed to deemphasize working with all
> chromosomes at once -- thus the
> introduction of getSS() to construct the smlSet for a selected set
> (typically only one) of chromosomes of SNP.
>
> Concisely computing and managing results from transcriptome x genome
> searches is addressed by
> the eqtlTests function and by genewiseFDRtab ... these functions are under
> development to simplify these
> tasks, which can be arduous as large imputed SNP panels come into play.
> Thus it is relevant to work with
> the devel branch as you start hitting limits. I will provide more news as
> work proceeds. As the initial discussion
> of this topic occurred on biostar list, I will note for other readers that a
> tutorial on using GGtools with R 2.14 is
> available at ismb11gg.wordpress.com, and that the ggtut experimental data
> package underlies the tutorial. Of
> note is that ggtut will not pass check with R devel, because some serialized
> objects conflict with revised class
> definitions. This will be sorted before too long.
>
>
>>
>> -- output of sessionInfo():
>
>
> I strongly advise you to upgrade to R 2.14. My sessionInfo for the runs
> above is
>
> R version 2.14.0 Patched (2011-11-09 r57622)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C
> [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591
> [5] LC_MONETARY=en_US.iso88591 LC_MESSAGES=en_US.iso88591
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines stats graphics grDevices datasets tools utils
> [8] methods base
>
> other attached packages:
> [1] illuminaHumanv1.db_1.12.1 GGtools_4.1.8
> [3] ff_2.2-3 bit_1.1-7
> [5] GenomicRanges_1.6.2 org.Hs.eg.db_2.6.4
> [7] rtracklayer_1.14.2 RCurl_1.7-0
> [9] bitops_1.0-4.1 IRanges_1.12.1
> [11] annotate_1.32.0 AnnotationDbi_1.16.2
> [13] GGBase_3.15.2 genefilter_1.36.0
> [15] RSQLite_0.10.0 DBI_0.2-5
> [17] snpStats_1.4.0 Matrix_1.0-1
> [19] lattice_0.20-0 survival_2.36-10
> [21] BiocGenerics_0.1.0 Biobase_2.14.0
> [23] weaver_1.20.0 codetools_0.2-8
> [25] digest_0.5.1 BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.22.0 BSgenome_1.22.0 grid_2.14.0 Rsamtools_1.7.1
> [5] XML_3.4-3 xtable_1.6-0 zlibbioc_1.0.0
>
>>
>>
>> > sessionInfo()
>> R version 2.13.1 (2011-07-08)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>>
>> attached base packages:
>> [1] tools splines stats graphics grDevices utils datasets
>> [8] methods base
>>
>> other attached packages:
>> [1] GGtools_3.10.2 ff_2.2-3 bit_1.1-7
>> [4] GenomicRanges_1.4.8 org.Hs.eg.db_2.5.0 rtracklayer_1.12.5
>> [7] RCurl_1.6-10 bitops_1.0-4.1 IRanges_1.10.6
>> [10] annotate_1.30.1 AnnotationDbi_1.14.1 GGBase_3.12.0
>> [13] RSQLite_0.10.0 DBI_0.2-5 snpStats_1.2.1
>> [16] Matrix_0.999375-50 lattice_0.19-33 survival_2.36-9
>> [19] Biobase_2.12.2
>>
>> loaded via a namespace (and not attached):
>> [1] Biostrings_2.20.4 BSgenome_1.20.1 grid_2.13.1 XML_3.4-3
>> [5] xtable_1.5-6
>>
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>
>
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