Last updated: 2020-01-27

Checks: 5 1

Knit directory: hgen471/

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Getting data

library(tidyverse)
work.dir ="~/Downloads/hapmap/"

## qqunif function
source("https://gist.githubusercontent.com/hakyim/38431b74c6c0bf90c12f/raw/21fbae9a48dc475f42fa60f0ef5509d071dea873/qqunif")

Download plink for mac


## Download plink from https://www.cog-genomics.org/plink2
## wget http://s3.amazonaws.com/plink1-assets/plink_mac_20200121.zip


## TODO: move plink executable to ~/bin/ 
## add to the path if necessary
## export PATH="$PATH:~/bin/"

Download HapMap data


refdir=~/Downloads/hapmap
mkdir $refdir
cd $refdir

mkdir output

## Download plink format hapmap 3 genotype data
## http://www.sanger.ac.uk/resources/downloads/human/hapmap3.html
wget -r ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2010-05_phaseIII/plink_format/ (This also downloads tar-ed individual population ped/map files)
##wget ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2010-05_phaseIII/plink_format/hapmap3_r3_b36_fwd.consensus.qc.poly.map
##wget ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2010-05_phaseIII/plink_format/hapmap3_r3_b36_fwd.consensus.qc.poly.ped
# FINISHED --2018-01-26 10:46:48--
# Total wall clock time: 3m 56s
# Downloaded: 4 files, 2.5G in 3m 56s (10.9 MB/s)
## remove annoying DS_Store files in OSX
## find . -name '.DS_Store' |xargs rm
## Mac OSX needs command line toos + homebrew installed. 
## then run 
## brew update
## brew install wget
## cd and use tabs to get to subfolder where gz files are

mv ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2010-05_phaseIII/plink_format/* $refdir
rm -rf ftp.ncbi*
gunzip *.gz

Download population data


## get reported population data
wget ftp://ftp.ncbi.nlm.nih.gov/hapmap/phase_3/relationships_w_pops_051208.txt

Create small bed/bim/fam file 

## create binary plink file for chr 22 (to have small example)
plink --file hapmap3_r3_b36_fwd.consensus.qc.poly --make-bed --chr 22 --out hapmapch22

## get superpopulation data
wget https://www.dropbox.com/s/yozrzsdrwqej63q/phase3_corrected.psam?dl=1 
mv phase3_corrected.psam\?dl\=1 phase3_corrected.psam

Calculate Fst among populations

plink --bfile hapmapch22 --fst --within relationships_w_pops_051208.txt --mwithin 5 --out output/hapmapch22-all

Calculate Fst among sub-populations

## create list of EUR, AFR, 

reldata = read_tsv(paste0(work.dir, "relationships_w_pops_051208.txt"))
samdata = read_tsv(paste0(work.dir,"phase3_corrected.psam"),guess_max = 2500) ## guess_max set to large number so that R reader consideres non numeric PAT and MAT values
names(samdata)[names(samdata)=="$IID"] = "IID"
superpop = samdata %>% select(SuperPop,Population) %>% unique()
eur = reldata %>% inner_join(superpop, by=c("population"="Population")) %>% filter(SuperPop=="EUR")
afr = reldata %>% inner_join(superpop, by=c("population"="Population")) %>% filter(SuperPop=="AFR")
eas = reldata %>% inner_join(superpop, by=c("population"="Population")) %>% filter(SuperPop=="EAS")

reldata %>% inner_join(superpop, by=c("population"="Population")) %>% count(population, SuperPop) %>% arrange(SuperPop)

Write list of EUR, EAS, AFR individuals

write_tsv(eur, paste0(work.dir,"EUR.sam"))
write_tsv(afr, paste0(work.dir,"AFR.sam"))
write_tsv(eas, paste0(work.dir,"EAS.sam"))

## plink --bfile hapmapch22 --fst --keep EUR.sam  --within relationships_w_pops_051208.txt --mwithin 5 --out hapmapch22-EUR

plink --bfile hapmapch22 --fst --keep AFR.sam  --within relationships_w_pops_051208.txt --mwithin 5 --out output/hapmapch22-AFR
plink --bfile hapmapch22 --fst --keep EUR.sam  --within relationships_w_pops_051208.txt --mwithin 5 --out output/hapmapch22-EUR
plink --bfile hapmapch22 --fst --keep EAS.sam  --within relationships_w_pops_051208.txt --mwithin 5 --out output/hapmapch22-EAS


sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.3.0 Rcpp_1.0.2      digest_0.6.19   rprojroot_1.3-2
 [5] backports_1.1.4 git2r_0.25.2    magrittr_1.5    evaluate_0.14  
 [9] rlang_0.4.1     stringi_1.4.3   fs_1.3.1        rmarkdown_1.13 
[13] tools_3.6.0     stringr_1.4.0   glue_1.3.1      xfun_0.7       
[17] yaml_2.2.0      compiler_3.6.0  htmltools_0.4.0 knitr_1.23