expand {IRanges}R Documentation

The expand method for uncompressing compressed data columns

Description

Expand an object with compressed columns such that all compressed values are represented as separate rows.

Usage

## S4 method for signature 'DataFrame'
expand(x, colnames, keepEmptyRows = FALSE)

Arguments

x

A DataFrame containing some columns that are compressed (e.g., CompressedCharacterList), or a Vector with compressed columns in mcols(x).

colnames

A character or numeric vector containing the names or indices of the compressed columns to expand. The order of expansion is controlled by the column order in this vector. This defaults to all of the recursive (list-like) columns in x (or mcols(x)).

keepEmptyRows

A logical indicating if rows containing empty values in the specified colnames should be retained or dropped. When TRUE, empty values are set to NA and all rows are kept. When FALSE, rows with empty values in the colnames columns are dropped.

Value

A DataFrame that has been expanded row-wise to match the dimension of the uncompressed columns.

Author(s)

Herve Pages and Marc Carlson

See Also

DataFrame-class

Examples

aa <- CharacterList("a", paste0("d", 1:2), paste0("b", 1:3), c(), "c")
bb <- CharacterList(paste0("sna", 1:2),"foo", paste0("bar",1:3),c(),"hica")
df <- DataFrame(aa=aa, bb=bb, cc=11:15)

## expand by all list-like columns (aa, bb), dropping empty rows
expand(df)

## expand the aa column only, and keep rows adjacent to empty values
expand(df, colnames="aa", keepEmptyRows=TRUE)

## expand the aa column only but do not keep rows
expand(df, colnames="aa", keepEmptyRows=FALSE)

## expand the aa and then the bb column, but
## keeping rows next to empty compressed values
expand(df, colnames=c("aa","bb"),  keepEmptyRows=TRUE)

## expand the bb and then the aa column, but don't keep rows adjacent to
## empty values from bb and aa
expand(df, colnames=c("aa","bb"), keepEmptyRows=FALSE)
[Package IRanges version 2.4.4 Index]