Mega2R (version 1.0.7)

init_SKAT: 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.

See Also

Mega2SKAT

Examples

# NOT RUN {
db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = init_SKAT(db, verbose = FALSE, allMarkers = FALSE)
ls(ENV)

# }