what is the actual genotype of SNP876?

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avrajit
Posts: 4
Joined: Thu May 07, 2015 10:03 am

what is the actual genotype of SNP876?

Postby avrajit » Tue May 19, 2015 6:06 am

Hi all
I am a new user of GenABEL. so far I found it very robust and well explained with a good tutorial support. But when I was trying as.character(gtdata(mydata)[1:4, 4] I'm not getting A/A or A/B or B/B kind of output . I am getting 1/1, 1/2 or /3/3 etc. what is the mistake I'm doing?
my sessionInfo()

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R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252    LC_MONETARY=English_India.1252
[4] LC_NUMERIC=C                   LC_TIME=English_India.1252   

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

other attached packages:
[1] GenABEL_1.8-0      GenABEL.data_1.0.0 MASS_7.3-40       

loaded via a namespace (and not attached):
[1] tools_3.1.2

mydata
genoD.txt

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A101 A102 A103 A104 A105 A106 A107
SNP212 SNP312 SNP222 SNP565 SNP121 SNP311 SNP876
1 2 1 2 1 1 1
2341 34352 4510 56151 67161 56151 61117
3 3 2 3 2 1 1
2 2 1 2 1 2 1
3 1 1 2 1 3 1
2 2 3 3 1 3 2
3 2 2 1 1 1 2
2 2 1 1 3 3 1
1 2 1 1 2 1 1

i converted it to raw using convert.snp.text()
phenodata.dat

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"id" "sex" "height" "width" "mass"
"A101" 0 3.4 6 10
"A102" 1 8.9 7 11
"A103" 1 8 3 7
"A104" 0 2.3 4 5
"A105" 1 3.5 4 6
"A106" 0 5.5 6 7
"A107" 0 5.6 6 8

i combined two files using

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mydata<- load.gwaa.data(phenofile, genofile, force=T, makemap=F, sort=T)

please help me
Last edited by lckarssen on Fri May 22, 2015 8:14 am, edited 1 time in total.
Reason: Reformatted output with the [code] tag

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