User: Sam

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Sam3.2k
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Posts by Sam

<prev • 468 results • page 1 of 47 • next >
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Answer: A: Replacing NA values of a column using values from another column
... 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 Sam3.2k
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Comment: C: Plot GWAS p value distribution for multiple traits
... 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 Sam3.2k
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Answer: A: Re-joining sample ID's and snp information from bgen files for analysis in R
... 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 Sam3.2k
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Answer: A: PRSice: how to obtain exact list of SNPs used for PRSice.best
... 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 Sam3.2k
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Comment: C: Fold change instead of expression (intensity values) in co-expression network?
... 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 Sam3.2k
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Comment: C: How to perform GWAS using BOLT-LMM iteratively for many phenotypes in bash
... That depends on your job submission system ...
written 5 weeks ago by Sam3.2k
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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 Sam3.2k
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Comment: C: is it possible to know individual genotype(alleles) by SNP in plink?
... `--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 Sam3.2k
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Answer: A: is it possible to know individual genotype(alleles) by SNP in plink?
... plink --bfile --extract --recode --out This should generate the desired output ...
written 6 weeks ago by Sam3.2k
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Comment: C: Correcting the Negative beta coefficient (genetic risk score )
... 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 Sam3.2k

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Scholar 6 weeks ago, created an answer that has been accepted. For A: Annovar: how to update sequence length based on deletion size
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Epic Question 10 months ago, created a question with more than 10,000 views. For Normalization Of Rna Sequencing Counts (By Ercc / Gene Length)
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