User: Sheila
Sheila • 310
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Posts by Sheila
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... Hi@Vale, There are a couple things I'd check/try:
1. Check to make sure there is a single space as opposed to a tab between the FID and IID columns in IDlist.txt
2. Rename the duplicate IIDs to something like 2204DUP so that way you have unique subject IDs.
I hope that helps! ...
written 21 months ago by
Sheila • 310
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... Hi,
I would like to filter my dataset using a list of chromosome and basepair positions using plink.
I understand you can filter based on a list of SNP NAMES in plink:
plink --bfile filename --extract snpfilename.txt --make-bed --out new_filename
**What would be the way to do this with chro ...
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... Hi, I have a list of logCPM values for a long list of genes. I would like to calculate the read counts from these values. I see that in EdgeR there is a getCounts() function, however it requires the data be in a DGEList-class format. The logCPM values I have, unfortunately is older and was not p ...
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... I am doing QC for a GWAS analysis. I used pc-AIR and pc relate (two Bioconductor Packages) to determine the relatedness and population substructure of my given dataset. I compared it to 1000 genomes data and have a plot comparing the first two PCs in my PCA analysis. In general, what is the best ...
written 2.4 years ago by
Sheila • 310
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... Hi, I am trying to use Haploview to look at LD blocks. I am able to install and open Haploview, however, when I try to (a) check for updates or (b) download data directly from hapmap, Haploview says it cannot connect to the internet, but I do have internet! I've looked on the Broad website but the ...
written 2.4 years ago by
Sheila • 310
• updated
2.4 years ago by
Pierre Lindenbaum ♦ 124k
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... Hi!
I would like to complete a case/control analysis with two covariates (sex and age) in plink. Here is my model
Y = B0 + B1X1 + B2X2 + B3X3
where...
Y = Disease Status (0 or 1),
X1 = given SNP,
X2 = Sex,
X3 = Age
I have a few questions:
This was my command:
plink --bfile myfile --asso ...
written 2.6 years ago by
Sheila • 310
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... Thanks! I actually have the BP of each SNP! I'll try and start from there :) ...
written 2.6 years ago by
Sheila • 310
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... Hi!
In short, I have a list of SNPs that I would like to map to the closest gene within 1000kb. I am using the biomaRt package in R/Bioconductor. I am successfully able to map my SNPs to Genes but only with biomaRt's default bp flanking region (I beleive that is 100kb). Here are my commands to g ...
written 2.6 years ago by
Sheila • 310
• updated
2.6 years ago by
Emily_Ensembl ♦ 20k
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... Hi Floris! Thanks for your note. I actually figured it out :) I subsetted the existing fam file for the subjects I was interested in and then used that as the input for the --keep command. Thanks for your help though! ...
written 2.6 years ago by
Sheila • 310
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... Hi! I have a Plink gwas data set. All files are in binary format (.bed,.bim).
Before I get into details, here is my question: **How can I subset for subjects I am interested in using Plink?**
I am aiming to subset a group of individuals for my analysis, however when I run the following command my ...
written 2.6 years ago by
Sheila • 310
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