KMgene (version 1.3)

prepCoxKM: KM for Survival Traits in GWAS Data (fit null model)

Description

This function (CoxKM) is used to perform KM analysis (Chen et al., 2014) for survival traits in GWAS data

Usage

prepCoxKM(
  Z,
  formula,
  SNPInfo = NULL,
  snpNames = "Name",
  aggregateBy = "gene",
  data = parent.frame(),
  verbose = FALSE
)

Arguments

Z

A matrix of genotypes (class: matrix). rows correspond to individuals and columns correspond to SNPs. Use <U+2019>NA<U+2019> for missing values. The column names of this matrix should correspond to SNP names in the SNP information file.

formula

Base formula under null hypothesis (class: formula). For Cox models, the formula follows that of the coxph() function.

SNPInfo

SNP Info file (class: data.frame). Must contain fields given in <U+2019>snpName<U+2019> and <U+2019>aggregateBy<U+2019>.

snpNames

The field of SNPInfo where the SNP identifiers are found. (Default="Name")

aggregateBy

The field of SNPInfo on which the skat results were aggregated. (Default="gene")

data

The data file in which to find variables in the formula (class: data.frame).

verbose

Whether or not to print the progress bar (class: logical).

Value

output: object as input for FbKM