User: Lemire

gravatar for Lemire
Lemire590
Reputation:
590
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Trusted
Location:
Canada
Last seen:
1 month ago
Joined:
5 years ago
Email:
l*******@yahoo.ca

Posts by Lemire

<prev • 53 results • page 1 of 6 • next >
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Comment: C: 450k CpG strands in hg38
... Do you need the strand information, though? Once you liftOver the positions, if you find a G on the ref sequence at that position then it means the probe was targeting the C on the other strand (-). Only cytosines can be methylated. ...
written 8 weeks ago by Lemire590
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Comment: C: Correcting the Negative beta coefficient (genetic risk score )
... There are software (e.g. PRSice) that takes care of this automatically. ...
written 11 weeks ago by Lemire590
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Comment: C: Can Plink 1.07 set-hh-missing output VCF?
... you need: --recode vcf ...
written 11 weeks ago by Lemire590
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Answer: A: GT 2/3, or 3/3 or 2/2 in vcf
... From the vcf specification: "GT genotype, encoded as alleles values separated by either of ”/” or “|”, e.g. The allele values are 0 for the reference allele (what is in the reference sequence), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on." The ALT alleles a ...
written 4 months ago by Lemire590
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Comment: C: Boxplots and Time Series Data
... ANOVA (one-way) is the test for the equality of means in 3 or more groups. While the test is derived from between- and within-group variation, it's not a test of variance. To answer the boxplot question, the following is an illustration of what I think you want. Some fake data first: y<- r ...
written 5 months ago by Lemire590
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Answer: A: Adding dosage for a SNP as a covariate to a phenotype file
... This is something you can do with vcftools. E.g. assuming your dosage is DS: vcftools --gzvcf vcffile.vcf.gz --extract-FORMAT-info DS \ --snp rs12345 --out outputprefix and you will get a text file with your dosage information for that particular snp. ...
written 5 months ago by Lemire590
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Comment: C: How to perform classical HLA alleles association analysis
... I would suggest doing this in R. Check [this post][1] and the answer that I gave. [1]: https://www.biostars.org/p/408461 ...
written 5 months ago by Lemire590
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Answer: A: IDAT to VCF conversion
... Chapter 6 of GenomeStudio Genotyping module guide deals with cluster generation. https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/genomestudio/genomestudio-2-0/genomestudio-genotyping-module-v2-user-guide-11319113-01.pdf ...
written 5 months ago by Lemire590
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Comment: C: What is the relationship between PLINK --pca and --mds-plot in terms of % varian
... MDS, just like PCA, has as many dimensions as there are variables. I don't know the specifics of the implementation, but my guess is if you specify 10, it will likely just give you the first 10 dimensions. This means that if you ask for 10, and then 20 in a second run, the first 10 should be the sa ...
written 6 months ago by Lemire590
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Comment: C: What is the relationship between PLINK --pca and --mds-plot in terms of % varian
... You need ALL eigenvalues, not just the first 20. The default is to output just 20, but there are actually as many eigenvalues as you have samples. Count your number of samples, and pass that as argument. In practice, at some point the eigenvalues get really small, but depending on your sample size ...
written 6 months ago by Lemire590

Latest awards to Lemire

Scholar 8 months ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ
Scholar 10 months ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ
Scholar 2.7 years ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Non A T G C base in RefSeq zebrafish mRNA sequence
Popular Question 4.3 years ago, created a question with more than 1,000 views. For CELLULOID: tumor ploidy, cellularity, subclonal copy number events
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ
Scholar 4.9 years ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Scholar 5.0 years ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ

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