On Tue, Nov 29, 2011 at 5:20 AM, francy [guest] <guest@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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