splitByAnnotation: Split data into a list by annotation element.
In Genominator: Analyze, manage and store genomic data

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`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.

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

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).

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

See Genominator vignette for more information.

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