Below are instructions on how to extract single SNP data from large genetic datasets.
*.map, *.ped or *.bed, *.bim,*.fam)*.gen or its binary version: *.bgen)*.vcf.gz)More on genetic data file formats here.
If you work with sensitive (human) data (e.g. anything that contains an identifier of an individual), you occasionally want to share that data. The most straightforward way to do so is to send them by email (and yes - we are all guilty of that!). The problem arises, if the data get into wrong hands. Let's say you send the email accidentally to the wrong person. Or worse, without your knowledge, the email gets into the wrong hands.
The good news is, that there is a secure & handy solution for this. But let's first have a look at some other solutions.
| # satRdays Cardiff 2018 | |
| This is a brief write-up of my [satRdays Cardiff](http://cardiff2018.satrdays.org/) experience. | |
| First - what is a [**satRday**](http://satrdays.org/)? | |
| It is an awesome concept: attending an **R conference** organised by a **local RUG** on a **Saturday**. | |
| The [programme](http://cardiff2018.satrdays.org/#programme) in Cardiff had parallel sessions - tough decision-making to pick between promising talks! |
| ## ////////////////// | |
| ## FUTURE PACKAGE | |
| ## ////////////////// | |
| ## here is a function that sums up really slow | |
| ## --------------------------------------------- | |
| slow_sum <- function(vec) { | |
| SUM <- 0 |
Helpful links for developing R packages
The following is a guide on how to perform a phylogenetic principal component analysis.
The phylogenetic principal component analysis, short pPCA, has been proposed by Revell in 2009 and Jombart et al. 2010.
Jombart also implemented pPCA in the adephylo R-package.
| ## adding column N as last column to a file | |
| FILE=~/gwas.txt | |
| N=98 | |
| awk '$NF="98"' $FILE > tmp-file | |
| sed -e '1s/98/N/' tmp-file > tmp2-file |