Mega2R (version 1.0.7)

applyFnToRanges: 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

Examples

# NOT RUN {
  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)

# }