User: Joey

gravatar for Joey
Joey410
Reputation:
410
Status:
Trusted
Location:
Seattle
Website:
http://faculty.washing...
Scholar ID:
Google Scholar Page
Last seen:
2 years, 11 months ago
Joined:
7 years, 8 months ago
Email:
j*******@yahoo.com

Posts by Joey

<prev • 32 results • page 1 of 4 • next >
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Answer: A: PLINK: How to concatenate PED and MAP files into single data-frame?
... Look at the --recodeA option in PLINK v1.07 or --recode A option in PLINK v1.90. It might be what you want. Say you have example.fam, example.bim, example.bed something like plink --bfile example --recodeA --out recoded ...
written 3.0 years ago by Joey410
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Answer: A: Can someone give me explanation about the output of plink
... Changing my answer.Sam's correct. ...
written 3.1 years ago by Joey410
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Answer: A: Removing SNPs from .bed file?
... Use PLINK (either 1.07 or 1.90). Look at removing subset of SNPs in this page: http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml#exclude If you have a text file (say snplist.txt) with SNP rsIDs (no headers) containing the list of SNPs that need to be excluded from the SNP data set (example. ...
written 3.1 years ago by Joey410
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Answer: A: Plotting large PPI biological networks
... If you want a high resolution graph with a bunch of options, cytoscape (http://www.cytoscape.org/) is a very good option to do the whole thing.     ...
written 3.6 years ago by Joey410
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Comment: C: SNP scoring using PLINK
... We have some papers where we used the genetic risk score in a Mendelian randomization study. Which variables do you want me to explain? I will try my best. ...
written 3.7 years ago by Joey410
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Answer: A: SNP scoring using PLINK
... Can you do two double checks: a) Check if those SNPs are present in your genetic data (bed/bim/fam)? and  b) If they are present, the reference allelein your scoring file matches with either one of the alleles in the *.bim file.   -Joey ...
written 3.7 years ago by Joey410
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Tool for GWAS fo a longitudinal phenotype
... Is there any good tool out there for GWAS of a longitudinal phenotype? Something which can pergorm LME models or GEE models. I have tried the R package BOSS but it is quite buggy.  Thanks,  -Joey ...
gwas longitudinal data written 3.7 years ago by Joey410
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liftover using GWAS summary data and PLINK binary files (bed/bim/fam)
... Hi,  I have a GWAS summary data (chr, snp, bp beta, se etc.) file based on the 1000G Aug 2010 1000G imputation (GRCh37.p13). The genetic data for calculating LD was given to me in PLINK binary/best guess genotype format (bed/bim/fam) and was based on a newer imputation (1000G March 2012; GRCh38).  ...
gwas snp liftover plink written 4.3 years ago by Joey410 • updated 3.8 years ago by dora 90
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Answer: A: PLINK format to EIGENSTRAT format
... Already answered here. https://www.biostars.org/p/98512/#98595 ...
written 4.6 years ago by Joey410
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Number of pseudogenes in NCBI GRCh37
... I downloaded the  NCBI GRCh37 gene list from https://bitbucket.org/baderlab/fast/downloads. What is the best way to find out how many are pseudogenes in this list? I tried Biomart but I wasn't able to do a full merge. Thanks, -Joey ...
pseudogenes genes written 4.7 years ago by Joey410 • updated 4.7 years ago by Ashutosh Pandey11k

Latest awards to Joey

Popular Question 3.1 years ago, created a question with more than 1,000 views. For Snptest (Gen/Sample) Files To R
Scholar 3.1 years ago, created an answer that has been accepted. For A: Conversion tools for GWAS
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Rationale For Different Types Of Snp--> Gene Mapping For Pathway Analysis
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Complete Snp Gsea Solution?
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Rationale For Different Types Of Snp--> Gene Mapping For Pathway Analysis
Scholar 5.0 years ago, created an answer that has been accepted. For A: Conversion tools for GWAS
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Complete Snp Gsea Solution?
Appreciated 5.4 years ago, created a post with more than 5 votes. For A: Calculating Ibd Using R Package
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Help Regarding Conversion Of Imputed Data: Snptest Format To Plink
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Snptest (Gen/Sample) Files To R
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Complete Snp Gsea Solution?
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Calculating Ibd Using R Package
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Error Message Received When Converting Impute File Format To Bed/Ped Files (Plin

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