I think you might have read the documentation more clearly, but it is a
somewhat tricky function, so here are some pointers.

suppose we have dem2.txt as a tab-delimited file with the contents you
indicate

> cat(readLines("dem2.txt"), sep="\n")
BICF2G630100019 04-0677/J279    C       C
BICF2G630100032 04-0677/J279    T       T
BICF2G630100034 04-0677/J279    G       G
BICF2G630100043 04-0677/J279    A       A
BICF2G630100054 04-0677/J279    T       T
BICF2G630100063 04-0677/J279    T       C
BICF2G630100075 04-0677/J279    T       T
BICF2G63010009  04-0677/J279    G       G
BICF2G630100090 04-0677/J279    C       C

> dput(id)
c("04-0677/J279", "04-0677/J279", "04-0677/J279", "04-0677/J279",
"04-0677/J279", "04-0677/J279", "04-0677/J279", "04-0677/J279",
"04-0677/J279")
> dput(snp)
c("BICF2G630100019", "BICF2G630100032", "BICF2G630100034",
"BICF2G630100043",
"BICF2G630100054", "BICF2G630100063", "BICF2G630100075", "BICF2G63010009",
"BICF2G630100090")

Then

> nn = read.snps.long("dem2.txt", unique(id), snp, fields=c(snp=1,
sample=2, allele1=3, allele2=4), codes="nucleotide", sep="\t")
9 genotypes successfully read
> nn
A SnpMatrix with  1 rows and  9 columns
Row name:  04-0677/J279
Col names:  BICF2G630100019 ... BICF2G630100090

> sessionInfo()
R Under development (unstable) (2012-02-04 r58266)
Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)

locale:
[1]
en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-ASCII

attached base packages:
[1] splines   stats     graphics  grDevices datasets  utils     tools
[8] methods   base

other attached packages:
[1] snpStats_1.5.4      Matrix_1.0-4        lattice_0.20-0
[4] survival_2.36-12    BiocInstaller_1.3.7 weaver_1.21.0
[7] codetools_0.2-8     digest_0.5.1

loaded via a namespace (and not attached):
[1] grid_2.15.0



On Wed, Mar 7, 2012 at 10:16 AM, Liz Hare <doggene@earthlink.net> wrote:

> Hello,
>
> I am trying to read an Illumina final format .txt file (tab-delimited)
> into snpStats. The file contains 4 columns: snp, sample, allele 1, and
> allele 2. Some sample lines:
>
> BICF2G630100019 04-0677/J279    C       C
> BICF2G630100032 04-0677/J279    T       T
> BICF2G630100034 04-0677/J279    G       G
> BICF2G630100043 04-0677/J279    A       A
> BICF2G630100054 04-0677/J279    T       T
> BICF2G630100063 04-0677/J279    T       C
> BICF2G630100075 04-0677/J279    T       T
> BICF2G63010009  04-0677/J279    G       G
> BICF2G630100090 04-0677/J279    C       C
>
> I can't figure out from the documentation or vignette on data input how to
> specify that the alleles are in two columns.
>
> This doesn't work:
>
> > CanineHD <- read.long(file="filename",
> +                       fields=c(snp=1, sample=2, genotype=3, genotype=4),
> +                       verbose=TRUE)
> Data to be read from the file filename
> No confidence thresholds specified
> Genotype read as a single field of two characters (which specify the
> alleles)
> Initial scan of file
> First sample: 04-0677/J279
> First snp: BICF2G630100019
> Last snp: YNp1-608
> Last sample: 10-1160
> 96x173662 matrix to be read
> Reading genotypes from file
>        20%       40%       60%       80%       100%
> .........|.........|.........|**.........|.........|
> -Error in read.long(file = "filename",  :
>  at line 1: C (expecting a 2-character genotype field)
> In addition: Warning message:
> closing unused connection 3 (filename)
>
> So I tried:
>
> > CanineHD <- read.long(file="filename",
> +                       fields=c(snp=1, sample=2, genotype=3),
> +                       gcodes="\t", codes="nucleotide", verbose=TRUE)
> Error in read.long(file = "filename",  :
>  unused argument(s) (codes = "nucleotide")
> > CanineHD <- read.long(file="filename",
> +                       fields=c(snp=1, sample=2, genotype=3),
> +                       split="\t", verbose=TRUE)
> Data to be read from the file filename
> No confidence thresholds specified
> Genotype read as a single field of two characters (which specify the
> alleles)
> Initial scan of file
> First sample: 04-0677/J279
> First snp: BICF2G630100019
> Last snp: YNp1-608
> Last sample: 10-1160
> 96x173662 matrix to be read
> Reading genotypes from file
>        20%       40%       60%       80%       100%
> .........|.........|.........|**.........|.........|
> -Error in read.long(file = "filename",  :
>  at line 1: C (expecting a 2-character genotype field)
> In addition: Warning message:
> closing unused connection 12 (filename)
>
> Is there a keyword for alleles rather than genotypes? I tried substituting
> the word 'allele' but didn't get anywhere. I suspect I'm not understanding
> something in the Details section of the documentation.
>
> Thanks,
> Liz
>
> --
> Liz Hare PhD
> Dog Genetics LLC
> doggene@earthlink.net
> http://www.doggenetics.com
>
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