User: Yean

gravatar for Yean
Yean120
Reputation:
120
Status:
Trusted
Location:
Bangkok
Last seen:
1 day, 10 hours ago
Joined:
9 months ago
Email:
K**************@gmail.com

Posts by Yean

<prev • 24 results • page 1 of 3 • next >
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Answer: A: Selection of SNPs after imputation
... it depends on your goal, in my opinion. If you perform GWAS, I think you should keep all variants because novel variants could be associated with your studied phenotype. but if you calculate a genetic risk score, it is fine to keep only desired SNPs. ...
written 5 weeks ago by Yean120
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Answer: A: Best practice for finding all genes SNPs, etc. related to a disease or phenotype
... Apart from curious suggestion, you can automatically retrieve disease-associated SNPs from the GWAS catalog by R package, [gwasrapidd][1] [1]: http://%20https://academic.oup.com/bioinformatics/article/36/2/649/5543089 ...
written 10 weeks ago by Yean120
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File Format Conversion (GO::TermFinder to wide format)
... Hi all, I Just did GO Enrichment using GO::TermFinder via API (I need to perform via API due to reproducible code) and the report is something like The following gene(s) will be considered: YDL235C YPD1 YDL224C WHI4 YDL225W SHS1 YDL226C GCS1 YDL227C HO YDL228C YDL ...
go::termfinder written 3 months ago by Yean120
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Comment: A: How do I match two files using one column as reference?
... Check this post (in R) https://stackoverflow.com/questions/1299871/how-to-join-merge-data-frames-inner-outer-left-right ...
written 3 months ago by Yean120
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Answer: A: VCF file ID missing
... Check this: [How to get SNP identifiers from VCF file?][1] [1]: https://www.biostars.org/p/300169/ ...
written 3 months ago by Yean120
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Answer: A: Subsetting .vcf.gz based on .txt file
... What's about plink ? plink1.9 --vcf input.vcf.gz --extract snp.snplist --make-bed --out extract_snp ...
written 4 months ago by Yean120
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Comment: C: Reference Data Set Download from 1000 genomes
... Try SnpSift to annotate rsID based on **your position** in vcf file http://snpeff.sourceforge.net/SnpSift.html#annotate ...
written 4 months ago by Yean120
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Answer: A: How to avoid hardcoding in R? How to automatize R scripts?
... I don't know if my approach is the best one but I usually just use the argument in my script, and whenever I got new datasets in different path , new variables or whatever. I just simply change the path of file or variable via argument. Something like Rscript myscript.R arg1 arg2 arg3 Check ...
written 4 months ago by Yean120
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Comment: C: How to invent novel algorithm ?
... Thanks for both of your guidance :) I just have some more questions ... **Whenever the originals are not practical under certain circumstances or to account for cases not originally considered** The hardest part is to find an existing theory to tackle those problem and translate it into mathemati ...
written 4 months ago by Yean120
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How to invent novel algorithm ?
... Hi all, I am wondering what is **the basic idea** of modifying the original algorithm in order to develop novel algorithm. For example in genetic risk score calculation, the original equation is `GRS <- log(odd ratio) * (No. of risk allele)`. But, the extended ones can be found in [LDpred][1] ...
genetic risk score algorithms written 4 months ago by Yean120 • updated 4 months ago by Asaf8.4k

Latest awards to Yean

Supporter 4 months ago, voted at least 25 times.
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: How to avoid hardcoding in R? How to automatize R scripts?
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to avoid hardcoding in R? How to automatize R scripts?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to avoid hardcoding in R? How to automatize R scripts?

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