applyFnToMarkers: apply a function to the genotypes from a set of markers

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

apply a function to the genotypes from a set of markers

Description

A matrix of the genotypes for all the specified markers is generated. Then, the call back function, op, is called with the markers, NULL (for the range), and the 'environment'.

Usage

applyFnToMarkers(op      = function (markers, range, envir) {},
                markers_arg,
                envir = ENV)

Arguments

op	Is a function of three arguments. It will be called once by applyFnToMarkers in a try/catch context. The arguments are: markers Marker data for each marker in geno. A marker is a data frame with the following 5 observations: locus_link is the ordinal ranking of this marker among all loci locus_link_fill is the position of corresponding marker genotype data in the unified_genotype_table MarkerName is the text name of the marker chromosome is the integer chromosome number position is the integer base pair position of marker range NULL: to indicate no explicit range was specified. envir An 'environment' holding Mega2R data frames and state data.
markers_arg	a data frame with the following 5 observations: locus_link is the ordinal ranking of this marker among all loci locus_link_fill is the position of corresponding marker genotype data in the unified_genotype_table MarkerName is the text name of the marker chromosome is the integer chromosome number position is the integer base pair position of marker
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)
  show = function(m, r, e) {
      print(r)
      print(m)
      print(head(getgenotypes(m, envir = e)))
  }

   # apply function "show" to all genotypes > 5,000,000 bp
   applyFnToMarkers(show, ENV$markers[ENV$markers$position > 5000000,])

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