User: Sam
Sam • 3.3k
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Posts by Sam
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... have never worked with this phenotype so I don't have any idea. Their [document][1] on this also isn't very clear. If I have to guess based on information from the note section, which stated: The Bike Test consists of many phases. A phase is generally divided into number of stages. At various points ...
written 23 days ago by
Sam • 3.3k
3
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... what you want might be instead
f <- read.table(file = "GeneExpressionDataset_normalized.tsv", sep="\t", header=TRUE)
wt <- apply(f[,2:11], 1, mean)
TherA <- apply(f[,22:31], 1, mean)
(I am guessing that you are looking for the mean of each group for each row) ...
written 8 weeks ago by
Sam • 3.3k
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... I am not sure what your identifier column name is, but assuming it is "ID"
you can do
col <- c("ID", col)
And continue ...
written 10 weeks ago by
Sam • 3.3k
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... Assuming you are trying to extract the columns by column names, you can do the following with data.table
library(data.table)
col <- unlist(fread("column.txt", header=F))
count <- fread("count.txt")
extracted <- count[,col, with=F]
If you don't have data.table install, you ...
written 10 weeks ago by
Sam • 3.3k
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2
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180
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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 3 months ago by
Sam • 3.3k
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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 3 months ago by
Sam • 3.3k
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182
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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 3 months ago by
Sam • 3.3k
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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 3 months ago by
Sam • 3.3k
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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 3 months ago by
Sam • 3.3k
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405
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... That depends on your job submission system ...
written 4 months ago by
Sam • 3.3k
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