Last updated: 2020-01-30
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Knit directory: hgen471/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | e73a329 | Hae Kyung Im | 2020-01-27 | L6 examples |
| html | e73a329 | Hae Kyung Im | 2020-01-27 | L6 examples |
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/* $refdir
rm -rf ftp.ncbi*
gunzip *.gzDownload population data
## get reported population data
wget ftp://ftp.ncbi.nlm.nih.gov/hapmap/phase_3/relationships_w_pops_051208.txt
Create small bed/bim/fam file
## create binary plink file for chr 22 (to have small example)
plink --file hapmap3_r3_b36_fwd.consensus.qc.poly --make-bed --chr 22 --out hapmapch22
## get superpopulation data
wget https://www.dropbox.com/s/yozrzsdrwqej63q/phase3_corrected.psam?dl=1
mv phase3_corrected.psam\?dl\=1 phase3_corrected.psam
## problems with zsh in Catalina to download dropbox link
## zsh: no matches found:
## https://www.dropbox.com/s/yozrzsdrwqej63q/phase3_corrected.psam?dl=1
## problems downloading data from dropbox
## https://www.bartbusschots.ie/s/2019/06/12/bash-to-zsh-file-globbing-and-no-matches-found-errors/
## setopt NULL_GLOB
## This doesn't work
## This worked: pasted the dropbox link on browser url and downloaded fine
Calculate Fst among populations
plink --bfile hapmapch22 --fst --within relationships_w_pops_051208.txt --mwithin 5 --out output/hapmapch22-allCalculate Fst among sub-populations
## create list of EUR, AFR,
reldata = read_tsv(paste0(work.dir, "relationships_w_pops_051208.txt"))
samdata = read_tsv(paste0(work.dir,"phase3_corrected.psam"),guess_max = 2500) ## guess_max set to large number so that R reader consideres non numeric PAT and MAT values
names(samdata)[names(samdata)=="$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 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.2
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_1.5.0 Rcpp_1.0.3 rprojroot_1.3-2 digest_0.6.22
[5] later_1.0.0 R6_2.4.1 backports_1.1.5 git2r_0.26.1
[9] magrittr_1.5 evaluate_0.14 stringi_1.4.3 rlang_0.4.1
[13] fs_1.3.1 promises_1.1.0 whisker_0.4 rmarkdown_1.17
[17] tools_3.6.1 stringr_1.4.0 glue_1.3.1 httpuv_1.5.2
[21] xfun_0.11 yaml_2.2.0 compiler_3.6.1 htmltools_0.4.0
[25] knitr_1.26