Analysis with SnpSet object CRLMM package
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@chintan-vora-xcelris-4978
Last seen 7.1 years ago
Dear Mathew, I am new to genotyping data analysis using R. I was going through your package CRLMM. I used the commands "readIdatFiles" and "crlmmIllumina". I am now wondering what to do with SNPSet object. Can you please explain me how can I use this object further? -- Regards, Chintan Vora Sr. Research Associate Xcelris Labs Ltd. Old Premchandnagar Road, Bodakdev, Ahmedabad-380 054 India. Tel: +91-79-66197777/66311114 Fax: +91-79-66309341 Email: chintan.vora@xcelrislabs.com Website: www.xcelrisgenomics.com "Please don't print this e-mail unless you really need to. Save Paper, Save Trees" ---------------------------------------------------------------------- ---------- Disclaimer\ \ \ Any views or opinions presented in this...{{dropped:13}}
crlmm crlmm • 842 views
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@benilton-carvalho-1375
Last seen 18 months ago
Brazil/Campinas/UNICAMP
Say that your SnpSet object is called 'crlmmOutput', you can run: theCalls = calls(crlmmOutput) theConfs = confs(crlmmOutput) to get the genotype calls (1 - AA; 2 - AB; 3 - BB) and their respective confidence scores. b On 28 November 2011 09:32, Chintan Vora - Xcelris <chintan.vora at="" xcelrislabs.com=""> wrote: > Dear Mathew, > > I am new to genotyping data analysis using R. > I was going through your package CRLMM. I used the commands > "readIdatFiles" and "crlmmIllumina". > > I am now wondering what to do with SNPSet object. > > Can you please explain me how can I use this object further? > -- > > Regards, > Chintan Vora > Sr. Research Associate > Xcelris Labs Ltd. > Old Premchandnagar Road, > Bodakdev, Ahmedabad-380 054 India. > Tel: +91-79-66197777/66311114 > Fax: +91-79-66309341 > Email: chintan.vora at xcelrislabs.com > Website: www.xcelrisgenomics.com > > > > "Please don't print this e-mail unless you really need to. Save Paper, Save Trees" > > -------------------------------------------------------------------- ------------ > > Disclaimer\ \ ?\ Any views or opinions presented in this...{{dropped:13}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Thank you for quick reply. That is exactly what is required in analysis (i.e. confidence score and information on SNP type). I want my output to look like this for each sample: SNP Name Sample ID Allele1 - Top Allele2 - Top Allele1 - Forward Allele2 - Forward Chr Position SNP GC Score rs1000113 5109232032_R05C01 G G C C 5 150220268 [T/C] 0.87 rs10008492 5109232032_R05C01 A G T C 4 38442114 [T/C] 0.36 rs10008493 5109232032_R05C01 A G T C 4 65127855 [T/C] 0.91 rs10008494 5109232032_R05C01 A T T A 4 19118424 [T/A] 0.74 rs1001179 5109232032_R05C01 G G G G 11 34416806 [T/C] 0.96 This output is same as given by illumina software. I am looking for similar kind off information for SNP . How should I proceed further? Is it like annotating SNPs? Regards, Chintan Vora Sr. Research Associate Xcelris Labs Ltd. Old Premchandnagar Road, Bodakdev, Ahmedabad-380 054 India. Tel: +91-79-66197777/66311114 Fax: +91-79-66309341 Email: chintan.vora@xcelrislabs.com Website: www.xcelrisgenomics.com On 11/29/2011 07:36 PM, Benilton Carvalho wrote: > Say that your SnpSet object is called 'crlmmOutput', you can run: > > theCalls = calls(crlmmOutput) > theConfs = confs(crlmmOutput) > > to get the genotype calls (1 - AA; 2 - AB; 3 - BB) and their > respective confidence scores. > > b > > On 28 November 2011 09:32, Chintan Vora - Xcelris > <chintan.vora@xcelrislabs.com> wrote: >> Dear Mathew, >> >> I am new to genotyping data analysis using R. >> I was going through your package CRLMM. I used the commands >> "readIdatFiles" and "crlmmIllumina". >> >> I am now wondering what to do with SNPSet object. >> >> Can you please explain me how can I use this object further? >> -- >> >> Regards, >> Chintan Vora >> Sr. Research Associate >> Xcelris Labs Ltd. >> Old Premchandnagar Road, >> Bodakdev, Ahmedabad-380 054 India. >> Tel: +91-79-66197777/66311114 >> Fax: +91-79-66309341 >> Email: chintan.vora@xcelrislabs.com >> Website: www.xcelrisgenomics.com >> >> >> >> "Please don't print this e-mail unless you really need to. Save Paper, Save Trees" >> >> ------------------------------------------------------------------- ------------- >> >> Disclaimer\ \ \ Any views or opinions presented in this...{{dropped:13}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > ---------------------------------------------------------------------- ---------- Disclaimer\ \ \ Any views or opinions presented in this...{{dropped:13}}
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