Documentation in one file: vartools.pdf

Program description

vartools is an R-package that incorporates various variant association tests.

Installation

Make sure that you have a stable Internet connection and R and GCC installed. Download or clone from the GitHub, save it in some folder you wish.

$R CMD INSTALL vartools

In some cases you have to be a system administrator, so you need to compile vartools with the following command:

$sudo R CMD INSTALL vartools

Quick start

CMC test:

library(vartools)
pgdata <- as.matrix(read.table(system.file("extdata","phengen.dat",package="vartools"), as.is=T, skip = 1))
cmc.pvalue <- cmc(table=pgdata)
print(cmc.pvalue)

KBAC test:

library(vartools)
alpha <- 0.05
num.permutation <- 3000
quiet <- 1
alternative <- 1
maf.upper.bound <- 0.05

casectrl.dat <- read.table(system.file("extdata","phengen.dat",package="vartools"), skip = 1) 
kbac.pvalue <- kbac(table=casectrl.dat, alpha, num.permutation, quiet, maf.upper.bound, alternative)
print(kbac.pvalue)

C-alpha test:

library(vartools)
casectrl.dat <- read.table(system.file("extdata","phengen.dat",package="vartools"), skip = 1)    
calpha.stat <- calpha(casectrl.dat)
calpha.stat

CMC test:

library(vartools)
pgdata <- as.matrix(read.table(system.file("extdata","phengen.dat",package="vartools"), as.is=T, skip = 1))
cmc.pvalue <- cmc(table=pgdata)
print(cmc.pvalue)

VT test:

library(vartools)
?vt
casectrl.dat <- read.table(system.file("extdata","phengen2.dat",package="vartools"), skip = 1)
vt.stat <- vt(casectrl.dat)
vt.stat

RareCover test:

library(vartools)
?rarecover

casectrl.dat <- read.table(system.file("extdata","phengen.dat",package="vartools"), skip = 1)
rarecover.stat <- rarecover(casectrl.dat)
rarecover.stat

RBT:

library(vartools)
?rbt

casectrl.dat <- read.table(system.file("extdata","phengen.dat",package="vartools"), skip = 1)
rbt.stat <- rbt(casectrl.dat)
rbt.stat

Other tests

In addition, vartools offers SKAT, WSS, aSum tests.Please check the user manual to use them.