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Biostatistics and Bioinformatics Branch (BBB)

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Generalized Functional Linear Models for Gene-based Case-Control Association Studies

Example from SKAT

library(fda)
library(MASS)
library(SKAT)
library(Matrix)
library(globaltest)

source("C:/NICHD/Research/software/Fan/Gen_Func_Linear_Model/GFLM_web/GFLM_fixed_model.R")
source("C:/NICHD/Research/software/Fan/Gen_Func_Linear_Model/GFLM_web/GFLM_beta_smooth_only.R")

source("C:/NICHD/Research/software/Fan/Func_Linear_Model/FLM_web/FLM_FPCA.R")
source("C:/NICHD/Research/software/Fan/Func_Linear_Model/FLM_web/FLM_FPCA_no_position.R")

data = data(SKAT.example)
names(SKAT.example)
attach(SKAT.example)

pheno = y.b
geno = Z
covariate = X
pos = c(1:67)

order = 4
bbasis = 10
gbasis = 10
fbasis = 11
gfasis = 11

gflm_fixed_bspline_pvalue = gflm_fixed_model(pheno, mode = "Additive", geno, pos, order, bbasis, fbasis, gbasis, covariate, base = "bspline", interaction = FALSE)
gflm_fixed_bspline_pvalue

gflm_fixed_fspline_pvalue = gflm_fixed_model(pheno, mode = "Additive", geno, pos, order, bbasis, fbasis, gfasis, covariate, base = "fspline", interaction = FALSE)
gflm_fixed_fspline_pvalue

fit.beta.smooth.only.bs = gflm_beta_smooth_only(pheno, mode = "Additive", geno, pos, order, bbasis, covariate, base = "bspline", interaction = FALSE)
fit.beta.smooth.only.bs

fit.beta.smooth.only.fs = gflm_beta_smooth_only(pheno, mode = "Additive", geno, pos, order, fbasis, covariate, base = "fspline", interaction = FALSE)
fit.beta.smooth.only.fs

#############################

fpca.no.position = flm_fpca_no_position(pheno, mode = "Additive", geno, covariates = SKAT.example$X, kz = 20, kb = 10, smooth.cov=FALSE, family = "binomial")
fpca.no.position

fpca = flm_fpca(pheno, mode = "Additive", geno, covariates = SKAT.example$X, pos, kz = 20, kb = 10, smooth.cov=FALSE, family = "binomial")
fpca

Last Updated Date: 04/25/2014
Last Reviewed Date: 04/25/2014

Contact Information

Name: Dr Paul Albert
Chief and Senior Investigator
Biostatistics and Bioinformatics Branch
Phone: 301-496-5582
E-mail: albertp@mail.nih.gov

Staff Directory
Vision National Institutes of Health Home BOND National Institues of Health Home Home Storz Lab: Section on Environmental Gene Regulation Home Machner Lab: Unit on Microbial Pathogenesis Home Division of Intramural Population Health Research Home Bonifacino Lab: Section on Intracellular Protein Trafficking Home Lilly Lab: Section on Gamete Development Home Lippincott-Schwartz Lab: Section on Organelle Biology