User: Sheila

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Sheila260
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8 months, 3 weeks ago
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5 years, 7 months ago
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Posts by Sheila

<prev • 45 results • page 1 of 5 • next >
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Comment: C: Cannot remove subjects from Plink files
... 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 9 months ago by Sheila260
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Plink filtering with physical position using a text file
... 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 ...
plink written 13 months ago by Sheila260 • updated 7 months ago by amcheroo0
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Calculating the read counts from LogCPM values (EdgeR)
... 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 ...
R rna-seq written 13 months ago by Sheila260 • updated 13 months ago by Biostar ♦♦ 20
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Determining the subjects to use after obtaining a PC plot of population substructure
... 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 ...
gwas population stratification best practices written 17 months ago by Sheila260
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Haploview cannot connect to the internet?
... 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 ...
haploview ld written 17 months ago by Sheila260 • updated 17 months ago by Pierre Lindenbaum115k
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case control association analysis with covariates in plink?
... 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 ...
association covariates plink case-control written 19 months ago by Sheila260
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Comment: C: using biomaRt in R to annotate SNPs to Genes within 1000kb
... Thanks! I actually have the BP of each SNP! I'll try and start from there :) ...
written 19 months ago by Sheila260
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using biomaRt in R to annotate SNPs to Genes within 1000kb
... 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 ...
R biomart bioconductor annotation written 19 months ago by Sheila260 • updated 19 months ago by Emily_Ensembl16k
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Comment: C: Cannot remove subjects from Plink files
... 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 19 months ago by Sheila260
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Cannot remove subjects from Plink files
... 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 ...
gwas plink filtering written 19 months ago by Sheila260

Latest awards to Sheila

Epic Question 16 months ago, created a question with more than 10,000 views. For Obtaining The Snp Rs Number With The Chromosomal Position
Popular Question 16 months ago, created a question with more than 1,000 views. For What Kind Of Analysis Can Do You With Vcf Files?
Popular Question 17 months ago, created a question with more than 1,000 views. For What Kind Of Analysis Can Do You With Vcf Files?
Popular Question 19 months ago, created a question with more than 1,000 views. For What Kind Of Analysis Can Do You With Vcf Files?
Great Question 2.3 years ago, created a question with more than 5,000 views. For Combining Data Of Multiple Vcfs Into One.
Epic Question 2.3 years ago, created a question with more than 10,000 views. For Obtaining The Snp Rs Number With The Chromosomal Position
Popular Question 2.3 years ago, created a question with more than 1,000 views. For What Are The Main Uses Of A Consensus Sequence?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Subsetting Vcf Data In Plink/Seq
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Subsetting Vcf Data In Plink/Seq
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Subsetting Vcf Data In Plink/Seq
Great Question 2.6 years ago, created a question with more than 5,000 views. For Obtaining The Snp Rs Number With The Chromosomal Position
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Subsetting Vcf Data In Plink/Seq
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Obtaining The Snp Rs Number With The Chromosomal Position
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Combining Data Of Multiple Vcfs Into One.
Student 5.4 years ago, asked a question with at least 3 up-votes. For Subsetting Vcf Data In Plink/Seq

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