[BioC] Using as.geneSet in GeneticsBase - problems with gene.columns

[weiliang Qiu]

Hi Johannes,
I think the problem is because you missed ")" after "Allele2...Top"
when you called as.geneSet function.

I attached the sample R code, and log to this e-mail with your sample data.

Have a nice day!

Weiliang

On Thu, Mar 19, 2009 at 10:03 AM, Johannes Gulmann Madsen
<johannes at dsr.life.ku.dk> wrote:
> Hello
>
> Im a new user of Bioconductor and therefore also a new user of the package
> GeneticsBase. I have a dataframe looking like this (only a tiny bit of it):
>
>> b[1:10,]
>                  SNP.Name Sample.ID Allele1...Top Allele2...Top GC.Score
> 1      0_A2M_DS066406.1_15 602358305             G             G   0.8607
> 2       0_A2M_DS068238.1_4 602358305             G             G   0.8311
> 3     0_AARSL_DS061819.1_2 602358305             G             G   0.6840
> 4    0_ABCA1_DS062937.1_32 602358305             G             G   0.7499
> 5  0_ABCA1_DS073864.1_41_2 602358305             A             A   0.7900
> 6    0_ABCA1_DS073864.1_41 602358305             G             G   0.7383
> 7    0_ABCA1_DS078984.1_39 602358305             A             A   0.8360
> 8    0_ABCA1_DS082793.1_19 602358305             G             G   0.8440
> 9    0_ABCC10_DS066718.1_3 602358305             C             C   0.8859
> 10   0_ABCC6_DS063353.1_20 602358305             A             C   0.6117
>
> Its of class 'data.frame' and i want it converted to a 'geneset' using
> as.geneSet.
>
> So i tried:
>
> b2 <- as.geneSet(b, gene.columns=c("Allele1...Top", "Allele2...Top",
> format=c("adjacent")), because the "Allele1...Top" and "Allele2...Top" are
> (combined, thats why i want to use format=c("adjacent"), is that wrong?) my
> genotypes, but it won't work. Does any of you have any experience using
> 'as.geneSet', i can't find any examples on the net that looks like mine? My
> idea of the dataset is that i want to genotype each 'Sample.ID' like this (a
> simple example):
>
> Sample.ID 1:
> SNP1: AA 0
>      AC 1
>      CC 2
>
> Sample.ID 2:
> SNP1: AA 0
>      AC 1
>      CC 2
>
> So I want to make sure that the same SNP on different Sample.ID's is genotyped
> the same way (like illustrated above).
>
> Hope you can help me.
>
> Regards Johannes
>
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-------------- next part --------------
SNP.Name Sample.ID Allele1.Top Allele2.Top GC.Score
"0_A2M_DS066406.1_15" 602358305             "G"             "G"   0.8607
"0_A2M_DS068238.1_4" 602358305             "G"             "G"   0.8311
"0_AARSL_DS061819.1_2" 602358305             "G"             "G"   0.6840
"0_ABCA1_DS062937.1_32" 602358305             "G"             "G"   0.7499
"0_ABCA1_DS073864.1_41_2" 602358305             "A"             "A"   0.7900
"0_ABCA1_DS073864.1_41" 602358305             "G"             "G"   0.7383
"0_ABCA1_DS078984.1_39" 602358305             "A"             "A"   0.8360
"0_ABCA1_DS082793.1_19" 602358305             "G"             "G"   0.8440
"0_ABCC10_DS066718.1_3" 602358305             "C"             "C"   0.8859
"0_ABCC6_DS063353.1_20" 602358305             "A"             "C"   0.6117