Description Usage Arguments Details Value References Examples
This is implementation for the Variable Threshold statistical test. It assigns different weights to rare variants base on their frequencies.
1 |
table |
a numeric matrix with first column having disease status '0' or '1' and the rest columns codes the locus genotype as '0', '1', and '2'. |
maf |
numeric value indicating the minor allele frequency threshold for rare variants (must be a positive number between 0 and 1, |
perm |
positive integer that defines the number of permutations, |
....
A list with the following elements:
vt.stat |
VT statistic |
perm.pval |
permuted p-value |
args |
descriptive information with number of controls, cases,variants, and permutations |
name |
name of the statistic |
Price AL, Kryukov GV, de Bakker PIW, Purcell SM, Staples J, Wei LJ, Sunyaev SR (2010) Pooled Association Tests for Rare Variants in Exon-Sequencing Studies. The American Journal of Human Genetics, 86: 832-838
1 2 3 4 5 6 7 | # Load the package
library(vartools)
?vt
casectrl.dat <- read.table(system.file("extdata","phengen2.dat",package="vartools"), skip = 1)
vt.stat <- vt(casectrl.dat)
vt.stat
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