[BioC] gwSnpTests in GGtools
guest at bioconductor.org
Tue Nov 29 11:20:36 CET 2011
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"
My first question is, why is the 'gwSnpTests' not working?
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 toâ¦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!
-- output of sessionInfo():
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
attached base packages:
 tools splines stats graphics grDevices utils datasets
 methods base
other attached packages:
 GGtools_3.10.2 ff_2.2-3 bit_1.1-7
 GenomicRanges_1.4.8 org.Hs.eg.db_2.5.0 rtracklayer_1.12.5
 RCurl_1.6-10 bitops_1.0-4.1 IRanges_1.10.6
 annotate_1.30.1 AnnotationDbi_1.14.1 GGBase_3.12.0
 RSQLite_0.10.0 DBI_0.2-5 snpStats_1.2.1
 Matrix_0.999375-50 lattice_0.19-33 survival_2.36-9
loaded via a namespace (and not attached):
 Biostrings_2.20.4 BSgenome_1.20.1 grid_2.13.1 XML_3.4-3
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