summarizeByAnnotation {Genominator} | R Documentation

## Summarize data based on genome annotation.

### Description

This function creates a summarization of columns of the data using specified SQLite functions, applying these summarization function to regions defined in an annotation data frame.

### Usage

    summarizeByAnnotation(expData, annoData,
      what = getColnames(expData, all = FALSE), fxs = c("TOTAL"),
      groupBy = NULL, splitBy = NULL, ignoreStrand = FALSE, bindAnno = FALSE,
      preserveColnames = TRUE, 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 data columns to be summarized.
`fxs` | Vector of strings giving the names of SQLite functions to call on the data column(s).
`groupBy` | Character vector refering to a column in `annoData`. Regions will be aggregated over distinct values of this column. Setting this argument will set `bindAnno` to `TRUE`. If `splitBy` is set, `meta.id` will override.
`splitBy` | String indicating column of `annoData` object on which to split results.
`ignoreStrand` | Logical indicating whether strand should be taken into account in aggregation. If `TRUE` strand will be ignored.
`bindAnno` | Logical indicating whether annotation information should be included in the output.
`preserveColnames` | Logical indicating whether column names should be preserved. Only possible when a single function is being applied.
`verbose` | Logical indicating whether details should be printed.

### Details

Most of the computation is done using SQLite. Depending on the use case, this approach may be significantly faster and use much less memory than the alternative: use `splitByAnnotation` to retrieve a list with all the data and then use R to summarize over each element of the list. It is (naturally) constrained to the use of operations expressible in (SQLite) SQL.

If `meta.id` is set to a column in `annoData`, all regions with the same value of the `meta.id` will be joined together; a standard use case is labelleing exons of a gene.

### Value

If `splitBy` is not specified, returns a data frame containing results of aggregation functions performed on each region defined in `annoData`. If `splitBy` is specified, returns a list of data frames with one entry for each unique value of the column which was split on.

### Author(s)

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

### References

The SQLite website http://www.sqlite.org/lang_aggfunc.html has details on what mathematical functions are implemented.

### See Also

See `Genominator` vignette for more information, as well as the `ExpData-class`.

### Examples

    ed <- ExpData(system.file(package = "Genominator", "sample.db"),
                  tablename = "raw")
    data("yeastAnno")
    summarizeByAnnotation(ed, yeastAnno[1:50,])

[Package Genominator version 1.34.0 Index]