Many thanks for your help and aplogies for not cc'ing  "
bioconductor@stat.math.ethz.ch", I forgot to select reponse to all.

I will try to resolve the problem with my PED files.

I also found this link which is very useful
http://www.biostat.harvard.edu/~carey/copenGG.html

best regards,
C

On Thu, Apr 1, 2010 at 5:43 AM, Vincent Carey <stvjc@channing.harvard.edu>wrote:

> Please read the posting guide and do not break the thread from the list.
> More will learn from the dialogue, and you may have the benefit of expertise
> of other readers who know more about SNP file formats than I do.
>
> Clearly this is not a problem with GGtools.  You have a ped file that
> read.snps.pedfile cannot process.  This is one of the drawbacks of using
> file formats that lack formal validators that can give specific indications
> on format violations.  I cannot see the flaw in the ped file based on your
> excerpt, but see below.
>
>
> On Wed, Mar 31, 2010 at 10:38 PM, claire pujoll <cpujoll@gmail.com> wrote:
>
>>
>> Dear Prof Carey,
>>
>> many thanks for your time and quick response.
>>
>> I read your two papers discussing the data structures for genetics of gene
>> expression. I think it will be useful to add a note in the new manuel to
>> tell the reader that smlSet has be replaced by racExSet as there as several
>> tutorial and vignette on the web discussing racExSet.
>>
>
> I will revise the vignette to indicate that the former racExSet class is
> superseded by the smlSet class.
>
>
>>
>> # GWAS data
>> setwd("home/hamming/SNPmatrix")
>> map  <-  read.pedfile.map("Filt_CommonSNPChrom24.map")
>> ped  <-  read.snps.pedfile("Filt_CommonSNPChrom24.ped")
>>
>>
>> # Gene expression data
>> library("wp5Express")
>> data(wp5Express)
>> es <- exprs(wp5Express)
>>
>> ## Create smlSet class
>> smlSetTest <- make_smlSet(es,                        # Gene expression
>>                            sml,                                      # SNP
>> data
>>                            organism = "Homo sapiens")
>>
>>
>> I tried to read SNP data but I had an error. Please note that I have PED
>> and MAP by chromosome and
>> also .txt genotype file with SNP as columon and row as individuals.
>>
>> > ped  <-  read.snps.pedfile("Filt_CommonSNPChrom24.ped")
>> Found accompanying map file, reading it first
>> Reading Filt_CommonSNPChrom24.ped ...
>> Can take a while...
>> Found 32 fields in the header, i.e. 13 snps, hopefully...
>> malformed input line: [CXMA-01-001      CXMA-01-001     0       0
>> 1       2       C T     A C     C C     T T     G G     A G     G T     G
>> T     C T     G G     C T     C C     A C
>> ...]
>> Error in read.snps.pedfile("Filt_CommonSNPChrom24.ped") :
>>   ped file invalid - see error message above
>>
>>
> You must try to make a valid ped file for your data.  Here is an example of
> a valid one:
>
> 1 1 0 0 1  1  A A  G T
> 2 1 0 0 1  1  A C  T G
> 3 1 0 0 1  1  C C  G G
> 4 1 0 0 1  2  A C  T T
> 5 1 0 0 1  2  C C  G T
> 6 1 0 0 1  2  C C  T T
>
> it is test.ped from the plink distribution
>
> It seems to me that having hyphenated text in the second column, as in your
> example, may be problematic.
>
> the associated map file is:
>
> 1 snp1 0 1
> 1 snp2 0 2
>
>
> if we apply read.snps.pedfile to test.ped, we see
>
> > mys = read.snps.pedfile("test.ped")
>
> Found accompanying map file, reading it first
> Reading test.ped ...
> Can take a while...
> Found 10 fields in the header, i.e. 2 snps, hopefully...
> last line [5] : 6 1 0 0 1  2  C C  T...
> EOF reached after 6 samples
> Read 6 samples from input, now converting...
> ...done, 6 samples with 2 snps
> > mys
> $snp.data
> A snp.matrix with  6 rows and  2 columns
> Row names:  Family.1.Individual.1 ... Family.6.Individual.1
> Col names:  snp1 ... snp2
>
> $subject.support
>                       Family Member Father Mother  Sex   Affected
> Family.1.Individual.1      1      1     NA     NA Male Unaffected
> Family.2.Individual.1      2      1     NA     NA Male Unaffected
> Family.3.Individual.1      3      1     NA     NA Male Unaffected
> Family.4.Individual.1      4      1     NA     NA Male   Affected
> Family.5.Individual.1      5      1     NA     NA Male   Affected
> Family.6.Individual.1      6      1     NA     NA Male   Affected
>
> $snp.support
>      snp.names position chromosome assignment
> snp1      snp1        1          1        A/C
> snp2      snp2        2          1        G/T
>
> Let us make an smlSet using this and related information.  First we need an
> ExpressionSet
> instance
>
> ex = matrix(rnorm(12), nr=2)  # fake expression data
> rownames(ex) = c("A", "B")
> es = new("ExpressionSet", exprs=ex)
> es$x = rnorm(6)  # fake covariate
>
> of course more metadata should be supplied, but at this point
>
> > es
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 2 features, 6 samples
>   element names: exprs
> protocolData: none
> phenoData
>   sampleNames: 1, 2, ..., 6  (6 total)
>   varLabels and varMetadata description:
>     x: NA
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation:
>
> now make the smlSet:
>
>  msl = make_smlSet(es, list(`1`=mys$snp.data))
>  sampleNames(msl) = rownames(mys$snp.data)
>
> we need a name on the snp matrix list elements, to enumerate chromosomes --
> you can use any relevant tokenization.  for most examples, we have one named
> element per chromosome, but other organizations (such as a single snp.matrix
> that is genome-wide) are possible
>
> once this is in hand, we can perform tests:
>
> > f1 = gwSnpTests(probeId("A")~x, msl, chrnum("1"))
> Warning messages:
> 1: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
> 2: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
> > topSnps(f1)
>          p.val
> snp2 0.1470954
> snp1 0.9257000
>
> ignore the warnings
>
> > sessionInfo()
> R version 2.11.0 Under development (unstable) (2010-03-24 r51388)
> x86_64-apple-darwin10.2.0
>
> locale:
> [1] C
>
> attached base packages:
> [1] splines   stats     graphics  grDevices datasets  tools     utils
> [8] methods   base
>
> other attached packages:
>  [1] GGtools_3.5.71      ff_2.1-2            bit_1.1-3
>  [4] annotate_1.25.0     AnnotationDbi_1.9.6 GGBase_3.7.7
>  [7] RSQLite_0.8-4       DBI_0.2-5           Biobase_2.7.5
> [10] snpMatrix_1.11.2    survival_2.35-7     weaver_1.13.0
> [13] codetools_0.2-2     digest_0.4.1
>
> loaded via a namespace (and not attached):
>  [1] BSgenome_1.15.18    Biostrings_2.15.25  GSEABase_1.9.0
>  [4] GenomicRanges_0.0.9 IRanges_1.5.74      RCurl_1.3-0
>  [7] XML_2.6-0           annaffy_1.19.0      graph_1.25.1
> [10] multicore_0.1-3     rtracklayer_1.7.12  xtable_1.5-5
> Warning messages:
> 1: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
> 2: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
>
>
>
>
>
>
>
>>
>>
>> many thanks for your help,
>>
>> best regards,
>> Claire
>>
>>
>>
>>
>>
>>
>>
>> On Thu, Apr 1, 2010 at 3:16 AM, Vincent Carey <stvjc@channing.harvard.edu
>> > wrote:
>>
>>> Dear Claire,
>>>
>>> If you are seeing references to racExSet, you are looking at an outdated
>>> version of the GGtools package.  The GGBase package includes a function
>>> make_smlSet that helps create the structure.  As you note, the snpMatrix
>>> package defines the snp.matrix class.  The snpMatrix package has functions
>>> that generate snp.matrix instances from ped format, hapmap-formatted data,
>>> plink-formatted data, or chiamo-formatted data.  If you do not use any of
>>> these formats, you will have to create a list of snp.matrix objects, each
>>> element created according to specifications in the snpMatrix package.
>>>
>>> If you have up-to-date versions of the software and would like further
>>> guidance, provide a small excerpt of your genotyping data file and I will
>>> provide illustration of how to create the associated smlSet, using some
>>> dummy expression and phenotype data.  Clearly the most convenient approach
>>> will be based on a conventional format for genotyping data such as those
>>> enumerated above.
>>>
>>>
>>> On Wed, Mar 31, 2010 at 8:29 PM, claire pujoll <cpujoll@gmail.com>wrote:
>>>
>>>> Dear Prof Carey, dear Bioconductor user,
>>>>
>>>>  Could you please tel me where can I find a clear tutorial on how
>>>> creating an smlSet class so I can use GGtools (I read the vignettes but
>>>> still not able to find clear information regarding snp data). For gene
>>>> expression I can create an eSet but how can I create SNP data slot from my
>>>> genotype file. I know That I should use snp.matrix but could we have an
>>>> example (not based on HapMap data).
>>>>
>>>> also it would be useful to clarify regarding racExSet and smlist as this
>>>> is realy very confusing
>>>>
>>>>
>>>> I have 3 matrices:
>>>>
>>>> gene expression (log2 scale)
>>>>                indiv1              indiv2    ...        indiv 1000
>>>>
>>>> probe1       .....
>>>>
>>>> probe2
>>>>
>>>> probe 48,000  .....
>>>>
>>>>
>>>> SNP data
>>>>                        SNP1          SNP2         SNP 700,000
>>>> indiv1                  AA            AB               BB
>>>> indiv2
>>>> .....
>>>> indiv1000           .....            .......             ......
>>>>
>>>> and pheno data
>>>>
>>>> thanks for your help.
>>>>
>>>>
>>>> best regards,
>>>>
>>>> Claire Pujoll, PhD
>>>>
>>>>
>>>>
>>>
>>
>

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