wtest (version 3.0)

hf: Parameters calculation for adjustment of W-test

Description

Function to estimate parameters (h and f) for W-test

Usage

hf(data, w.order, B = 400, n.sample = nrow(data),
  n.marker = "default.nmarker")

Arguments

data

a data frame or matrix contains genotypes in the columns. Genotypes should be coded as (0, 1, 2) or (0, 1).

w.order

a numeric number taking values 1 or 2. If w.order = 1, main effect is calculated. If w.order = 2, pairwise interaction effect is calculated.

B

a numeric number specify the number of replicates. Default is 400.

n.sample

a numeric number specify the number of samples to be involved for estimating parameters. Default is the total number of samples in the data.

n.marker

a numeric value, the number of biomarkers to use in bootstrapping. Default is the minumn value of total number of markers and 1,000 markers for order =1, and 50 markers for order =2.

Value

a set of parameters indexed by k, obtained automatically. For main effect, k is the number of levels of a predictor variable. For pairwise interactions, k is the number of categorical combinations of a pair.

References

Maggie Haitian Wang, Rui Sun, Junfeng Guo, Haoyi Weng, Jack Lee, Inchi Hu, Pak Sham and Benny C.Y. Zee (2016). A fast and powerful W-test for pairwise epistasis testing. Nucleic Acids Research.doi:10.1093/nar/gkw347.

See Also

wtest, w.diagnosis, w.qqplot

Examples

# NOT RUN {
data(mydata)

# Please note that parameter B is recommended to be greater than 400.
# For high order interaction analysis (w.order > 2), it is recommended to use default n.sample.
hf1<-hf(data = mydata, w.order = 1, B = 100)
hf2<-hf(data = mydata, w.order = 2, B = 80)
# }