User: hessjl

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hessjl50
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New User
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United States
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3 years, 2 months ago
Joined:
5 years, 2 months ago
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h*****@lemoyne.edu

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Posts by hessjl

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Command Plink in R (for loop)
... As general interest to know if R can do this, since it's my go-to language.  ...
written 3.9 years ago by hessjl50
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Command Plink in R (for loop)
... I'll first layout the block of R code that I'm working on: for( i in 1:length(input_names)){ input_names[[i]] -> MYDATA system("./plink --noweb --bfile MYDATA --freq --out test[[i]]") } This will return an error as there is no file named "MYDATA" in the working directory. The point is that ...
R for loop written 3.9 years ago by hessjl50 • updated 3.9 years ago by PoGibas4.8k
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Comment: C: Plink: LD-clumping of .dosage/.fam files
... Thanks for bringing clarity to this!  ...
written 4.0 years ago by hessjl50
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Comment: C: Plink: LD-clumping of .dosage/.fam files
... Bummer! And do you know off hand of a program that converts the style of .dosage files I'm working with to say .ped? The --make-bed option doesn't produce anything valid :(   ...
written 4.0 years ago by hessjl50
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Plink: LD-clumping of .dosage/.fam files
...   Here's a breakdown of my situation. I'm trying to pass to pass the following command options in Plink: --dosage MY_DATA.dosage --fam MY_DATA.fam --clump GWASresults.assoc --clump-p1 1 --clump-p2 1  --clump-r2 0.1 --clump-kb 500 --out MY_DATA_CLUMPED Strangely, this returns an association summ ...
linkage dosage plink r2 clump written 4.0 years ago by hessjl50 • updated 4.0 years ago by chrchang5235.0k
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Plink error message: Misaligned SNPs in dosage files
... Hi all, I'm trying to run a mega-GWAS of multiple studies in Plink and came across the following error message:  ######################################## Skipping web check... [ --noweb ]  Writing this text to log file [ GWASoutput.log ]   Options in effect:     --noweb     --dosage combineDOS. ...
gwas plink written 4.0 years ago by hessjl50 • updated 2.2 years ago by Biostar ♦♦ 20
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Comment: C: Selecting SNPs to impute in Plink
... Thanks for this insight! As subtext, are you indicating that whole GWAS imputation is the way to go; or can I still pre-filter my reference set to expedite the imputation turnaround?  ...
written 4.5 years ago by hessjl50
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Selecting SNPs to impute in Plink
... Hi all, I want to construct a workflow that will allow me to impute small batches of SNPs that were untyped in my GWAS data (in .bed .bim .fam fomat).   Is it possible to meaningfully subset my reference panel (hapmap release 23) so that I only impute the ~8000 missing SNPs? Would it be erroneous ...
impute plink written 4.5 years ago by hessjl50 • updated 4.5 years ago by chrchang5235.0k
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Comment: C: Plink: Retrieving specific SNP data for individuals in dataset
... Thank you for the clear explanation chrchang523!  The last command you provided worked like a charm.   ...
written 4.8 years ago by hessjl50
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Plink: Retrieving specific SNP data for individuals in dataset
... I am new to plink and have a (hopefully) simple data management operation, but little idea of how to implement it.  The essentials are listed here:   I have three genotype call files:  data.bed, data.fam, and data.bim.  I created a file snps.txt containing a list of markers. My goal is to creat ...
plink written 4.8 years ago by hessjl50 • updated 4.8 years ago by Alex Reynolds28k

Latest awards to hessjl

Popular Question 3.5 years ago, created a question with more than 1,000 views. For Plink: Retrieving specific SNP data for individuals in dataset
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Plink: Retrieving specific SNP data for individuals in dataset

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