User: baggiohbs.1989

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Posts by baggiohbs.1989

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Answer: A: CNT in Plink allele score fuction issue
... For people who may have the same silly problem as me, I straightforwardly give the answer here. Suppose your ScoreFile has 1 line, rsID effect_allele beta 1:2245570 G -0.0276009 your GenotypingData.bim has a corresponding line ( ignore the ambiguous stran ...
written 6 months ago by baggiohbs.19890
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Plink scoring function mechanism
... To use `--score ScoreFile` function, in `ScoreFile`, we need SNP ID, effect allele and effect size. Say, if the effect allele is the minor allele, then the score contributed by the SNP should be `effective size * dosage (effect allele)`; however, if the effect allele is not the minor allele, then ho ...
scoring plink written 6 months ago by baggiohbs.19890
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Comment: C: CNT in Plink allele score fuction issue
... Say, as explained, CNT is about 2*#SNP. However, for CNT2, how to explain the discrepancy between CNT2 and either #SNP or 2*#SNP? I tested several subjects, and the missing rate of SNPs (unobserved SNPs from the naming list) is very low. For example, for all 1.5million SNPs interested, only ~20 SNPs ...
written 6 months ago by baggiohbs.19890
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Comment: C: CNT in Plink allele score fuction issue
... Thanks for your answer. If muliplying 2 is the case, then it makes sense. However, CNT2 is much less than CNT, so does that mean there are a portion of snps are not named? ...
written 6 months ago by baggiohbs.19890
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CNT in Plink allele score fuction issue
... The objective is to calculate the genetic risk score, given the genotyping data, effective allele and effective size. Totally 1.5 million SNPs are included in the bfile.bim, and they all have variant ID with form Chr:BP; e.g., 1:12345. However, after I submit the code /projects/bsi/gentools/bin ...
score plink written 7 months ago by baggiohbs.19890

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Scholar 6 months ago, created an answer that has been accepted. For A: CNT in Plink allele score fuction issue

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