init_SKAT: load Mega2 SQLite database and perform initialization for...

In Mega2R: Accessing and Processing a 'Mega2' Genetic Database

load Mega2 SQLite database and perform initialization for SKAT usage

Description

This populates the R data frames from the specified Mega2 SQLite database. It then prunes the samples to only include members that have a definite case or control status. Undefined samples are ignored.

Usage

init_SKAT(db = NULL, verbose = FALSE, allMarkers = FALSE, ...)

Arguments

db	specifies the path of a Mega2 SQLite database containing study data.
verbose	TRUE indicates that diagnostic printouts should be enabled. This value is saved in the returned environment.
allMarkers	TRUE means use all markers in a given transcript even if there is no variation. FALSE means ignore markers that show no variation; this is the default.
...	fed to dbmega2_import(); should be bpPosMap= to select from the maps of base pairs, if the default is not desired.

Value

"environment" containing data frames from an SQLite database and some computed values.

Note

init_SKAT creats a data frame, envir$phe, of phenotype observations. In addition, it initializes a matrix to aid in translating a genotype allele matrix to a genotype count matrix.

It also initializes the data frame envir$SKAT_results to zero rows.

See Also

Mega2SKAT

Examples

db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = init_SKAT(db, verbose = FALSE, allMarkers = FALSE)
ls(ENV)

Mega2R documentation built on May 29, 2024, 1:14 a.m.