README.md

In izhbannikov/vartools: Variant Association Tools R-package

vartools - Variant Association tools R-package

vartools offers nine varitan association tests:

• CMC: Combined and Multivariate Collapsing Method for Rare Variants
• KBAC: Kernel Based Adaptive Clustering Method
• RBT: Replication Based Test for Protective Variants
• VT: Variable Thresholds Test for Case Control Data Analysis
• RareCover: A "Covering Algorithm" for Rare and Low Frequency Variants
• C(alpha): C-alpha Test for Protective Variants
• WSS: Weighted Sum Statistic via Rank Test
• aSum: Data-adaptive Sum Test for Protective and Deleterious Variants
• SKAT: SNP-set (Sequence) Kernel Association Test Method

Installation

R CMD INSTALL vartools

Usage

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

VT

library(vartools)
?vt

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

RareCover

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

Contact

Ilya Y. Zhbannikov, [e-mail], [e-mail]

izhbannikov/vartools documentation built on May 18, 2019, 7:14 a.m.