User: Yean

gravatar for Yean
Yean80
Reputation:
80
Status:
Trusted
Location:
Bangkok
Last seen:
an hour ago
Joined:
5 months ago
Email:
K**************@gmail.com

Posts by Yean

<prev • 19 results • page 1 of 2 • next >
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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 10 hours ago by Yean80
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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 7 days ago by Yean80
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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 10 days ago by Yean80
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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 11 days ago by Yean80
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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 12 days ago by Yean80 • updated 11 days ago by Asaf7.6k
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Answer: A: Reference Data Set Download from 1000 genomes
... Please check [Kevin's tutorial][1] [1]: https://www.biostars.org/p/335605/ ...
written 13 days ago by Yean80
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Answer: A: Need help in making corrlation plot
... check this out [ComplexHeatmap][1]. The tutorial is quire easy to follow [1]: https://jokergoo.github.io/ComplexHeatmap-reference/book/index.html ...
written 4 weeks ago by Yean80
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Answer: A: Information content of gene ontology
... I think I found the answer which is using the annotation file (GO.db) from [bioconductor][1] This is an example code I have used (sorry for a bit messy) #if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") #BiocManager::install("GO.db") li ...
written 5 weeks ago by Yean80
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Information content of gene ontology
... Hi all I am struggling with calculating the information content of the individuals GO term. As far as i know, most R packages deal with the semantic similarity of GO term such as GOSemSim **but I didn't find any tools calculating IC of individuals GO term yet** Does anyone know the tools for ...
gene ontology information content written 5 weeks ago by Yean80
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Comment: C: How to represent genotypes of form 1|1
... You can convert your genotype file into PED/MAP format by plink For example plink1.9 --vcf your.vcf --recode --out example ...
written 4 months ago by Yean80

Latest awards to Yean

Supporter 4 days ago, voted at least 25 times.
Good Answer 9 days 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 10 days ago, created a post with more than 5 votes. For A: How to avoid hardcoding in R? How to automatize R scripts?
Teacher 10 days 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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