| init_pedgene {Mega2R} | R Documentation |
load Mega2 SQLite database and perform initialization for pedgene usage
Description
This populates the R data frames from the specified Mega2 SQLite database.
Usage
init_pedgene(db = NULL, verbose = FALSE, traitname = "default", ...)
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. |
traitname |
Name of the affection status trait to use to set the case/control status; default value = "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_pedgene calculates schaidPed and pedPer that are used later in the Dopedgene calculation. In addition, it initializes a matrix to aid in translating a genotype allele matrix to a genotype count matrix.
It also initializes the dataframe envir$pedgene_results to zero rows.
See Also
DOpedgene, Mega2pedgene, mkfam
Examples
db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = init_pedgene(db, traitname = "default")
ls(ENV)