cheuerde’s gists

cheuerde / slide_GWAS.r

Last active October 13, 2015 16:44

GWAS using sliding windows and likelihood ratio test

	# Claas Heuer, September 2015

	#####################################################
	### Likelihood ratio test for multiple regression ###
	#####################################################

	slide_GWAS <- function(y, M, X = NULL, verbose = TRUE, sliding_window=TRUE, window_size = 10) {

	library(lmtest)

cheuerde / compile_r_devel.sh

Last active September 14, 2015 16:23

Compile R-devel

	# Claas Heuer, September 2015

	# set default installation directory:
	INSTDIR=$HOME/opt

	# place to store the source packages
	SOURCES=$HOME/sourcebuilds

	###################
	### Compiling R ###

cheuerde / package_submit_cran.sh

Last active September 14, 2015 16:28

Submit R package to Cran

	# Claas Heuer, September 2015
	#

	# First check your package on your machine ('cpgen' is the package folder)

	R CMD check --as-cran cpgen

	# Nothing is allowed, not even 'NOTES' (but probably depends, one or two notes might be ok)

	# then check again using 'devtools'

cheuerde / mixture.r

Last active September 8, 2015 16:04

Mixture models in R using mixtools

	# Claas Heuer, September 2015
	#
	# Extremely good vignette for mixtools: https://cran.r-project.org/web/packages/mixtools/vignettes/mixtools.pdf

	library(mixtools)
	library(ks)

	########################
	### Gaussian Mixture ###
	########################

cheuerde / ggplot2_grid.r

Created September 3, 2015 16:25

ggplot2 - arrange plots in grid

	library(ggplot2)
	library(reshape2)
	library(gridExtra)

	dat <- read.csv("dat.csv",header=TRUE,stringsAsFactors=FALSE)

	# make flat file
	D <- melt(dat, id.vars=c("Reg.No.Id"),measure.vars=c("Tpi","Pl","Dpr"))

	# make the graphs

cheuerde / xlsx_to_csv.sh

Created September 2, 2015 18:10

convert excel xlsx to csv

cheuerde / awk_stuff.sh

Last active April 12, 2016 14:21

AWK and GREP stuff

	# Claas Heuer, Spetember 2015
	#
	# helpful:
	# http://www.grymoire.com/Unix/Awk.html#uh-1
	# http://www.shellhacks.com/en/Using-BASH-Grep-OR-Grep-AND-Grep-NOT-Operators



	# count number of lines
	awk -F',' 'END{print NR;}' test.csv

cheuerde / win_unix.sh

Created September 1, 2015 15:21

Windows File to Unix

	# first remove all carriage returns (https://kb.iu.edu/d/acux)
	#dos2unix Report.txt Report_unix.txt

	awk '{ sub("\r$", ""); print }' Report.txt > Report_unix.txt

cheuerde / glibc_install.sh

Last active April 24, 2024 08:06

Install GNU libc version parallel to existing system

	# Claas Heuer, August 2015
	#
	# urls:
	# http://stackoverflow.com/questions/847179/multiple-glibc-libraries-on-a-single-host
	# http://www.gnu.org/software/libc/download.html

	cd $HOME
	mkdir glibc_update
	cd glibc_update

cheuerde / mysql_dump.r

Last active August 29, 2015 14:28

Access SQL dump database in R

	# Claas Heuer, August 2015
	#
	# links:
	# http://www.rackspace.com/knowledge_center/article/installing-mysql-server-on-debian
	# http://www.thegeekstuff.com/2008/09/backup-and-restore-mysql-database-using-mysqldump/
	# https://mkmanu.wordpress.com/2014/07/24/r-and-mysql-a-tutorial-for-beginners/
	# http://stackoverflow.com/questions/15420999/rodbc-odbcdriverconnect-connection-error
	# http://www.w3schools.com/sql/sql_join.asp

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