User: Sam
Sam • 3.2k
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Posts by Sam
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... If you have data.table installed, and assuming your data is stored in `dat`
library(data.table)
dat <- as.data.table(dat)
dat[is.na(H1), H1:=H2]
should do
...
written 14 days ago by
Sam • 3.2k
0
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99
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... From the sound of it, you seems to be doing a phewas study. This package might be helpful https://pubmed.ncbi.nlm.nih.gov/24733291/ ...
written 21 days ago by
Sam • 3.2k
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99
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... You can try to convert the BGEN file into a VCF or uncompressed GEN fille and extract the SNPs / samples at the same time using QCTools developed by BGEN's author. ...
written 22 days ago by
Sam • 3.2k
1
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90
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... Use `--print-snp` which will generate a ***output prefix***.snp file. This file contain all the post-clump SNPs and their p-value. You can then filter out the SNPs included in the best score by filtering according to the p-value threshold ...
written 23 days ago by
Sam • 3.2k
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2.2k
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... Unfortunately, that was almost 5 years ago and I really have no memory of what that link was. Though I guess it might be something related to Network analyzer from UCSF? Something like http://www.cgl.ucsf.edu/home/scooter/CSB/Network_Analyzer_Handout.pdf
...
written 26 days ago by
Sam • 3.2k
0
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2
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226
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2
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... That depends on your job submission system ...
written 5 weeks ago by
Sam • 3.2k
1
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1
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183
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Comment:
C: Unused argument in R
... The parameters for rnorm is `rnorm(N, mean, sd)`. I guess what you are trying to do here is to generate multiple normally distributed values. For that you will need to do `replicate(Nreps, rnorm(N, n.mean, n.stdev))` in the `gen.norm.dat` function.
...
written 5 weeks ago by
Sam • 3.2k
1
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1
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155
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... `--recode` will generate the ped file, which split the genotype into two columns. With `--recode transpose` you will get one variant per column, where the fifth and sixth fields are allele calls for the first sample in the .tfam file ('0' = no call); the 7th and 8th are allele calls for the second i ...
written 6 weeks ago by
Sam • 3.2k
2
votes
1
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155
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1
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... plink --bfile --extract --recode --out
This should generate the desired output ...
written 6 weeks ago by
Sam • 3.2k
0
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0
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237
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... It is generally not recommend to use PRS as an instrument for MR as PRS likely contains pleiotropic effects, which breaks the basic assumption of MR.
On the other hand, you can use many different software for PRS calculation which usually handles the mismatch coding alleles and GWAS effective alle ...
written 6 weeks ago by
Sam • 3.2k
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