applyFnToRanges: apply a function to all the genotypes for markers found in...

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

apply a function to all the genotypes for markers found in several specified ranges

Description

First, for each range, determine the markers that fall between the start and end base pair of the range. Then, for each set of markers generate a matrix of the genotypes of those markers. Finally, the op function is called for each range with the arguments: markers, range, and 'environment'.

Usage

applyFnToRanges(op          = function (markers, range, envir) {},
                ranges_arg  = NULL,
                indices_arg = NULL,
                fuzz_arg    = 0,
                envir       = ENV)

Arguments

op	Is a function of three arguments. It will be called repeatedly by applyFnToRanges 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 An indicator of which range argument of applyFnToRanges these markers correspond to. envir An 'environment' holding Mega2R data frames and state data.
ranges_arg	is 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_arg	is a vector of 3 integers that specify the location of chromosome, start base pair column and end base pair column of the ranges_arg data frame. An optional fourth integer indicates the column containing the name of the ranges.
fuzz_arg	is an integer vector of length one or two. The first argument is used to reduce the start base pair selected from each range and the second to increase the end base pair position. (If only one value is present, it is used for both changes.) Note: The values can be positive or negative.
envir	an 'environment' that contains all the data frames created from the SQLite database.

Value

None

Note

If the ranges_arg and indices_arg are NULL or missing, then the default ranges that have been set by setRanges are used. If setRanges has not been called, a default set of the ranges is used.

Examples

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

  show = function(m, r, e) {
      print(r)
      print(m)
      print(head(getgenotypesraw(m, envir = e)))
  }

   # apply function "show" to all genotypes on chromosomes 1 for two base pair
   # ranges
   applyFnToRanges(show,
                   ranges_arg =
                   matrix(c(1, 2244000, 2245000,
                            1, 3762500, 3765000),
                           ncol = 3, nrow = 2, byrow = TRUE),
                   indices_arg = 1:3)

   # apply function "show" to all genotypes on chromosomes 1 for two base pair
   # ranges
   applyFnToRanges(show,
                   ranges_arg =
                   matrix(c(1, 2240000, 2245000, "range1",
                            1, 3760000, 3765000, "range2"),
                           ncol = 4, nrow = 2, byrow = TRUE),
                   indices_arg = 1:4)

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