Position error using write.plink

Question

[ida.larsson]

Hi, I am experiencing a problem when trying to use write.plink from the R-package snpStats. The output is three plink-files; .bed, .bim and .fam and the position of each SNP in the resulting .bim-file is completely wrong (see below).

1   rs6678176   0   5   A   G
1   rs78286437  0   7   C   T
1   rs72961022  0   17  C   T
1   rs12082355  0   46  C   T
1   rs11166268  0   53  A   C
1   rs12059609  0   73  A   G
1   rs6657921   0   92  C   G
1   rs7514596   0   115 C   G

In addition to the SnpMatrix with all genotypes (800 000 SNPs, 95 samples) I also give write.plink a subject.data dataframe containing info about the samples and a snp.data dataframe which contains info about the SNPs, e.g. chromosome and position. When I manually go through parts of snp.data the positions seems to be correct, so I guess the error occurs when using write.plink. This is my line of code for outputing the plink-files:

library("snpStats")

write.plink('plinkfromR', snps = snps, subject.data = famFile,
            pedigree = pedigree, id = id, father = father, mother = mother,
            sex = sex, phenotype = phenotype, snp.data = smc_test$map,
            chromosome = chromosome, genetic.distance = genetic.distance,
            position = position, allele.1 = allele.1, allele.2 = allele.2)

and here is the snp.data dataframe containing correct positions for the SNPs:

           chromosome genetic.distance  position allele.1 allele.2
rs6678176           1               NA 100000827        A        G
rs78286437          1               NA 100000843        C        T
rs72961022          1               NA 100003476        C        T
rs12082355          1               NA 100007454        C        T
rs11166268          1               NA 100008607        A        C
rs12059609          1               NA 100012794        A        G

I would be very grateful for any help or suggestions on how to resolve this. This is causing me a lot of errors later in my analysis!

Ida

[zx8754]

Are some arguments not supposed to be in quotes? E.g.: sex = "sex" ?

[ida.larsson]

That might be the case since it refers to the column names of the dataframes "famFile" and "smc_test$map", however I couldn't read that from the documentation and most of the info seems to be read correctly anyway (sex is for example correct in the output .fam file). But I can try changing and see what happens!

[Vivek]

Can you also post the map file you are using here? snp.data = smc_test$map

Is there a discordance between your snp.data and this map?

[ida.larsson]

the smc_test$map is the snp.data-file, so there should be no discordance, I posted a part of it above. Or am I misunderstanding something with the snp.data?

> head(smc_test$map)
           chromosome genetic.distance  position allele.1 allele.2
rs6678176           1               NA 100000827        A        G
rs78286437          1               NA 100000843        C        T
rs72961022          1               NA 100003476        C        T
rs12082355          1               NA 100007454        C        T
rs11166268          1               NA 100008607        A        C
rs12059609          1               NA 100012794        A        G