Lavinia Gordon | 24 Jan 03:29 2013
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Re: VariantAnnotation - MatrixToSnpMatrix - only returns NAs

Hi Valerie,
Just one other thought, is it possible that MatrixToSnpMatrix() cannot work with unphased data?  My VCF is
unphased.  If I change the file VariantAnnotation\extdata\chr22.vcf to unphased that gives all NA values.

> vcf <- readVcf("chr22.vcf", "hg19")
> calls <- geno(vcf)$GT
> a0 <- ref(vcf)
> a1 <- alt(vcf)
> mat <- MatrixToSnpMatrix(calls, a0, a1)
> head(t(as(mat$genotype, "character")))
            HG00096 HG00097 HG00099 HG00100 HG00101
rs7410291   "NA"    "NA"    "NA"    "NA"    "NA"   
rs147922003 "NA"    "NA"    "NA"    "NA"    "NA"   
rs114143073 "NA"    "NA"    "NA"    "NA"    "NA"   
rs141778433 "NA"    "NA"    "NA"    "NA"    "NA"   
rs182170314 "NA"    "NA"    "NA"    "NA"    "NA"   
rs115145310 "NA"    "NA"    "NA"    "NA"    "NA"   

With regards,

Lavinia Gordon
Senior Research Officer
Quantitative Sciences Core, Bioinformatics

Murdoch Childrens Research Institute
The Royal Children's Hospital
Flemington Road Parkville Victoria 3052 Australia 
T 03 8341 6221
www.mcri.edu.au

-----Original Message-----
From: Lavinia Gordon 
Sent: Thursday, 24 January 2013 8:47 AM
To: 'Valerie Obenchain'
Cc: bioconductor@...
Subject: RE: [BioC] VariantAnnotation - MatrixToSnpMatrix - only returns NAs

Hi Valerie,

Thank you for your reply.  I'll investigate the development branch option.
I did see the warnings however I find it hard to believe that these should apply to every single entry in my VCF.
With regards,

Lavinia Gordon
Senior Research Officer
Quantitative Sciences Core, Bioinformatics

Murdoch Childrens Research Institute
The Royal Children's Hospital
Flemington Road Parkville Victoria 3052 Australia T 03 8341 6221 www.mcri.edu.au

-----Original Message-----
From: Valerie Obenchain [mailto:vobencha@...]
Sent: Wednesday, 23 January 2013 4:14 PM
To: Lavinia Gordon
Cc: bioconductor@...
Subject: Re: [BioC] VariantAnnotation - MatrixToSnpMatrix - only returns NAs

Hi Lavinia,

If you can use the development branch MatrixToSnpMatrix() has been replaced by genotypeToSnpMatrix().
This is much more full featured and robust function. However if you are using the release branch you still
need to work with MatrixToSnpMatrix(). If this is the case, please read the man page at

?MatrixToSnpMatrix

This page outlines the cases for which the values will be NA.  You should be seeing warnings such as 'only
diploid calls are included', 'only single nucleotide variants are included' or 'variants with >1 ALT
allele are set to NA'. If you are not seeing such warnings, please send me a small sample of your VCF so I can
reproduce this problem.

Valerie

On 01/22/13 17:35, Lavinia Gordon wrote:
> Hi, I have just started working with VCF files and have discovered the VariantAnnotation package, many
thanks for making these functions available.
> Following the code outlined in the reference manual for MatrixToSnpMatrix, my VCF returns only NA values:
>> head(geno(vcf)$GT)
>             GHS008 GHS015 GHS025 GHS026 GHS027 GHS031 GHS033 GHS034 GHS036
> chrM:73    "1/1"  "0/0"  "1/1"  "0/0"  "0/0"  "1/1"  "0/0"  "0/0"  "0/0"
> chrM:119   "0/0"  "0/0"  "0/0"  "1/1"  "1/1"  "0/0"  "0/0"  "0/0"  "0/0"
> rs72619361 "0/0"  "1/1"  "0/0"  "0/0"  "0/0"  "0/0"  "1/1"  "1/1"  "1/1"
> chrM:150   "1/1"  "1/1"  "1/1"  "1/1"  "1/1"  "1/1"  "1/1"  "1/1"  "1/1"
> chrM:189   "0/0"  "0/0"  "0/0"  "1/1"  "1/1"  "0/0"  "0/0"  "0/0"  "0/0"
> chrM:195   "1/1"  "1/1"  "1/1"  "0/0"  "0/0"  "1/1"  "1/1"  "1/1"  "1/1"
>> head(t(as(mat$genotype, "character")))
>             GHS008 GHS015 GHS025 GHS026 GHS027 GHS031 GHS033 GHS034 GHS036
> chrM:73    "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"
> chrM:119   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"
> rs72619361 "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"
> chrM:150   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"
> chrM:189   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"
> chrM:195   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"   "NA"
>
> I have run the reference manual code with the supplied VCF and it all looks good.
> I have no reason to suspect that there is anything wrong with my VCF.
> Could anyone give me any tips as to how I can troubleshoot this and work out why all the NAs are appearing?
>
> Many thanks,
>
> Lavinia Gordon
> Senior Research Officer
> Quantitative Sciences Core, Bioinformatics
>
> Murdoch Childrens Research Institute
> The Royal Children's Hospital
> Flemington Road Parkville Victoria 3052 Australia T 03 8341 6221 
> www.mcri.edu.au
>
>> vcf
> class: VCF
> dim: 4665545 9
> genome: hg19
> exptData(1): header
> fixed(4): REF ALT QUAL FILTER
> info(19): AC AF ... SB EFF
> geno(5): AD DP GQ GT PL
> rownames(4665545): chrM:73 chrM:119 ... chrUn_gl000249:14244
>    chrUn_gl000249:16222
> rowData values names(1): paramRangeID
> colnames(9): GHS008 GHS015 ... GHS034 GHS036 colData names(1): Samples
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] snpStats_1.8.1          Matrix_1.0-10           lattice_0.20-13
>   [4] survival_2.37-2         VariantAnnotation_1.4.6 Rsamtools_1.10.2
>   [7] Biostrings_2.26.2       GenomicRanges_1.10.6    IRanges_1.16.4
> [10] BiocGenerics_0.4.0      BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
>   [1] AnnotationDbi_1.20.3   Biobase_2.18.0         biomaRt_2.14.0
>   [4] bitops_1.0-5           BSgenome_1.26.1        DBI_0.2-5
>   [7] GenomicFeatures_1.10.1 grid_2.15.2            parallel_2.15.2
> [10] RCurl_1.95-3           RSQLite_0.11.2         rtracklayer_1.18.2
> [13] stats4_2.15.2          tools_2.15.2           XML_3.95-0.1
> [16] zlibbioc_1.4.0
>
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