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xinhe-lab / mirage

Mixture model based Rare variant Analysis on Genes
https://xinhe-lab.github.io/mirage
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how to obtain the NO.case and NO.control #3

Open linnanqia opened 3 years ago

linnanqia commented 3 years ago

Dear, I still felt confused about how to obtain the NO.case and NO.control. You said that " (No.case, how many times the variant appears in cases, No.contr, how many times the variant appears in controls — you can compute these quantities from your data)". which file I can get this information. Can you give me an example?Thank you!

han16 commented 3 years ago

No.case and No.contr are total number of alleles in cases and controls at a genomic locus. These numbers are typically very small in rare variant analysis. Hope this helps.

linnanqia commented 3 years ago

Hi， dear， Is it true to obtain the NO.case and NO.control?

NO.case

grep 0/1

count_case_01 <- data.frame(apply(tmp_vcf_case_data,1,function(x) length(grep('0/1',x)))) rownames(count_case_01) <- tmp_vcf_case_data[,1] colnames(count_case_01) <- "count_01"

grep 1/2

count_case_12 <- data.frame(apply(tmp_vcf_case_data,1,function(x) length(grep('1/2',x)))) rownames(count_case_12) <- tmp_vcf_case_data[,1] colnames(count_case_12) <- "count_12"

I am waiting for your response! Many Thanks!

--

谭海珠 Haizhu Tan
汕头大学医学院 Shantou University Medical School

在 2021-03-13 04:54:25，"Shengtong" @.***> 写道：

No.case and No.contr are total number of alleles in cases and controls at a genomic locus. These numbers are typically very small in rare variant analysis. Hope this helps.

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han16 commented 3 years ago

I am not sure about your sample but the data is passed along to me from bioinformaticians.