mkMarkers: create "markers" data frame

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

Description

Create the markers data frame. It contains 5 observations:

locus_link:

locus offset of this marker

locus_link_fill:

locus offset plus an accumulating fudge factor that jumps with each new chromosome because the count of markers per chromosome is force to be a multiple of 4. (This value corresponds to the offset of the marker in the unified_genotype_table.)

MarkerName:

name of the marker

chromosome:

chromosome number of the marker

position:

base pair position of the marker (selected by bpPosMap[below])

Usage

mkMarkers(bpPosMap = 1, envir = ENV)

Arguments

bpPosMap	An integer that indicates the map (index) to use to merge the chromosome/position fields from the map_table data frame to the marker_table data frame. See showMapNames() for the string name to index mapping.
envir	an environment that contains all the data frames created from the SQLite database.

Details

Select a map (index) from the map_table to merge with the select marker_table data frame to make the marker data frame. See showMapNames() for the string name to index mapping.

Value

None

Examples

db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = read.Mega2DB(db, verbose = FALSE)

mkMarkers(1)

ENV$markers

Mega2R documentation built on Dec. 11, 2021, 9:12 a.m.