blockassoc: Association tests for blocks of genotypes (one by one)

In tobyjohnson/gtx: Genetics ToolboX

Description

Calculations association test statistics for each genetic variant in a block.

Usage

blockassoc(qcall, data, minimac,
usubjid = getOption("gtx.usubjid", "USUBJID"), 
threshold.MAF = 0, threshold.Rsq = 0, threshold.pass = NULL,
message.begin = "blockassoc", out.signif = 6, use.compiled = FALSE)
## S3 method for class 'lm'
blockstats(m1, m0, coefname = "GENOTYPE")
## S3 method for class 'glm'
blockstats(m1, m0, coefname = "GENOTYPE")
## S3 method for class 'coxph'
blockstats(m1, m0, coefname = "GENOTYPE")
## S3 method for class 'clm'
blockstats(m1, m0, coefname = "GENOTYPE")

Arguments

qcall	A quoted call to a model fitting function
data	Data frame (phenotype data) in which qcall is to be evaluated
minimac	Path to minimac inputed genotype info and dosages
usubjid	Name of the unique subject id variable in data
threshold.MAF	Minimum minor allele frequency (MAF) for inclusion in output
threshold.Rsq	Minimum imputation quality (Rsq) for inclusion in output
threshold.pass	Character vector of SNP names to include in output independent of MAF or Rsq
message.begin	Optional text to begin each progress message with
out.signif	Number of significant digits for output
use.compiled	Flag whether to use fast C++ code for special cases
m1	Fitted model object with genotype term
m0	Fitted model object without genotype term
coefname	Name of the coefficient for genotype in m1

Details

TO BE WRITTEN

TO DO - Add arguments for genotypes to be an existing data frame, PLINK binary or –recodeA output, or VCF

Value

Returns a data frame with info and association statistics.

Author(s)

Toby Johnson [e-mail]

Examples

## Not run: 
library(ordinal)
library(survival)
library(MASS)

write.table(blockassoc(quote(lm(simCount ~ sexMale + PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10)),
                       data = read.table("phenotypes/simCount.pheno", header = TRUE, as.is = TRUE),
                       minimac = "imputed-20120314/chr22chunk6",
                       threshold.MAF = 0.01, threshold.Rsq = 0.5),
            file = "test-lm.out", row.names = FALSE, quote = FALSE)

write.table(blockassoc(quote(glm(simCount ~ sexMale + PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10,
family = poisson)),
                       data = read.table("phenotypes/simCount.pheno", header = TRUE, as.is = TRUE),
                       minimac = "imputed-20120314/chr22chunk6",
                       threshold.MAF = 0.01, threshold.Rsq = 0.5),
            file = "test-glm.out", row.names = FALSE, quote = FALSE)

write.table(blockassoc(quote(clm(factor(simCount) ~ sexMale + PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10)),
                       data = read.table("phenotypes/simCount.pheno", header = TRUE, as.is = TRUE),
                       minimac = "imputed-20120314/chr22chunk6",
                       threshold.MAF = 0.01, threshold.Rsq = 0.5),
            file = "test-clm.out", row.names = FALSE, quote = FALSE)

write.table(blockassoc(quote(coxph(Surv(simLife, simSurv) ~ sexMale + PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10)),
                       data = read.table("phenotypes/simLife.pheno", header = TRUE, as.is = TRUE),
                       minimac = "imputed-20120314/chr22chunk6",
                       threshold.MAF = 0.01, threshold.Rsq = 0.5),
            file = "test-coxph.out", row.names = FALSE, quote = FALSE)

## End(Not run)

tobyjohnson/gtx documentation built on Aug. 30, 2019, 8:07 p.m.