User: nadrianam

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nadrianam30
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Posts by nadrianam

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Rsamtools to separate vcf file by chromosome?
... I'm using Rsamtools to try and separate a vcf file by chromosome and while there are plenty of questions answered using samtools/vcftools/etc, I can't seem to adapt them to work in R. (I'm using Windows so I'm stuck to using R). I also have Rbamtools but that doesn't seem to have a split function. ...
vcf rsamtools chromosome written 2.6 years ago by nadrianam30
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Using snpStats to read a pedfile, object 'm' not found
... Hello, I'm using snpStats on R to try and read a pedfile and keep running into an issue. I input this: > read.pedfile("test.ped") And get this: Error in read.pedfile("test.ped") : object 'm' not found Any idea what 'm' is? I imagine it's a type of variable in the script that convert ...
R plink ped written 2.6 years ago by nadrianam30 • updated 16 months ago by Kevin Blighe44k
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Reading a .ped file in R?
... I apologize if this is incredibly asinine, but how can I view my ped file as a matrix in R? I've been using plink to do some analyses on a bunch of chip-seq data we have, but we want to separate the cases from the two studies that make up our dataset. I plan on utilizing some sort of "if, else" func ...
R plink ped written 2.6 years ago by nadrianam30 • updated 16 months ago by fatmasayed930

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