User: gunnhelenmoen

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Posts by gunnhelenmoen

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plink/GCTA: How to remove multiple SNPs and a range around them
... Hi! I have a list of around 200 SNPs that I wan't to remove from my plink file. I also want to remove about 1 MB around each of these SNPs. My problem is: using the --exclude flag only removes the SNPs using --exclude-snp and --window allow me to remove the SNP and the window I would also be ope ...
genome snp plink gcta written 9 months ago by gunnhelenmoen0 • updated 9 months ago by chrchang5237.3k
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Comment: C: Exctracting genotype data on a single SNP from all individuals in a dataset
... The impute dataset would look something like this: --- 22:16050075:A:G 16050075 A G --- 22:16050115:G:A 16050115 G A --- 22:16050213:C:T 16050213 C T --- rs367963583:16050922:T:G 16050922 T G each line would be followed by the the probabillity for the genototype for each individua ...
written 2.1 years ago by gunnhelenmoen0
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Exctracting genotype data on a single SNP from all individuals in a dataset
... I want to exstract a single SNP from my .impute file (created using IMPUTE2). I want this information as a plink file with genotype on all in individuals in the study at this particular posistion. When working with non-imputed data I've used this command line: ./plink --bfile GWASfile --snps rs ...
genome gene snp written 2.1 years ago by gunnhelenmoen0
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Genotype information on illumina EPIC chip using the meffil package
... Hi! I'm trying to make the genotype file from the Illumina EPIC chip using the meffil package. This is the documentation: In R: writeLines(meffil.snp.names(), con="snp-names.txt") In the UNIX command shell (you will need plink1.90, available here) plink --bfile dataset --extract snp-n ...
R written 2.3 years ago by gunnhelenmoen0 • updated 2.2 years ago by EagleEye6.7k
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Illumina EPIC methylation analysis with meffil
... I'm trying to run quality control on the new Illumina EPIC chip methylation data with the meffil packages. I've used it with the Illumina 450k previously and then I've used the following command: qc.parameters <- meffil.qc.parameters(beadnum.samples.threshold = 0.1, ...
R methylation illumina epic meffil written 2.4 years ago by gunnhelenmoen0 • updated 2.3 years ago by Biostar ♦♦ 20

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