setRanges: set default range data: chromosome and start/end base pair

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

set default range data: chromosome and start/end base pair

Description

This function sets the default list of ranges used by applyFnToRanges. applyFnToRanges examines each range and the set of markers that fall within the range will be processed.

Usage

setRanges(ranges, indices, envir = ENV)

Arguments

ranges	a data frame that contains at least 4 observations: a name, a chromosome, a start base pair position and an end base pair position.
indices	a vector of 3 or 4 integers that specify the chromosome column, start base pair, column and end base pair column of range data frame and lastly the name column. If the vector only contains 3 integers, a name will be generated from the three range elements and it will be appended to the ranges and the last range column will be added to the indices.
envir	an 'environment' that contains all the data frames created from the SQLite database.

Value

None

Examples

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

ranges = matrix(c(1, 2240000, 2245000,
                  1, 2245000, 2250000,
                  1, 3760000, 3761000,
                  1, 3761000, 3762000,
                  1, 3762000, 3763000,
                  1, 3763000, 3764000,
                  1, 3764000, 3765000,
                  1, 3765000, 3763760,
                  1, 3763760, 3767000,
                  1, 3767000, 3768000,
                  1, 3768000, 3769000,
                  1, 3769000, 3770000),
                 ncol = 3, nrow = 12, byrow = TRUE)

setRanges(ranges, 1:3)

ENV$refRanges

ranges = matrix(c(1, 2240000, 2245000,
                  1, 2245000, 2250000,
                  1, 3760000, 3761000,
                  1, 3761000, 3762000,
                  1, 3762000, 3763000,
                  1, 3763000, 3764000,
                  1, 3764000, 3765000,
                  1, 3765000, 3763760,
                  1, 3763760, 3767000,
                  1, 3767000, 3768000,
                  1, 3768000, 3769000,
                  1, 3769000, 3770000),
                 ncol = 3, nrow = 12, byrow = TRUE)
ranges = data.frame(ranges)
ranges$name = LETTERS[1:12]
names(ranges) = c("chr", "start", "end", "name")

setRanges(ranges, 1:4)

ENV$refRanges

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