R: Split data into a list by annotation element.

splitByAnnotation {Genominator}

R Documentation

Split data into a list by annotation element.

Description

This function splits the data into a list of matrices, by annotation element.

Usage

splitByAnnotation(expData, annoData, what = "*",
  ignoreStrand = FALSE, expand = FALSE, 
  addOverStrands = FALSE, verbose = getOption("verbose"))

Arguments

`expData`	An object of class `ExpData`.
`annoData`	A data frame which must contain the columns `chr`, `start`, `end` and `strand` which specifies annotation regions of interest.
`what`	Vector of names of columns of `expData` to be included in output.
`ignoreStrand`	Logical indicating whether strand should be ignored. If `TRUE`, data that falls into the annotation region, regardless of strand, is included.
`expand`	Logical indicating whether positions with no data should be included in output. If `TRUE`, lines are added to the output to give a value for each position, even if this value is 0.
`addOverStrands`	Logical indicating whether data should be added across strands. Only applies when `expand` is `TRUE`.
`verbose`	Logical indicating whether details should be printed.

Details

This function retrieves the data contained in the regions of the annoData object. The return object may be significant in size.

Value

Returns a list of length equal to the number of annotation entries split upon. Each list element is either a matrix of data, or a list with data matrices for each strand included (if expand is TRUE and addOverStrands is FALSE).

Author(s)

James Bullard bullard@berkeley.edu, Kasper Daniel Hansen khansen@jhsph.edu

Examples

ed <- ExpData(system.file(package = "Genominator", "sample.db"),
              tablename = "raw")
data("yeastAnno")
splitByAnnotation(ed, yeastAnno[1:30,])

[Package Genominator version 1.34.0 Index]