genoset (version 1.28.2)

RleDataFrame-class: Class "RleDataFrame"

Description

The RleDataFrame class serves to hold a collection of Run Length Encoded vectors (Rle objects) of the same length. For example, it could be used to hold information along the genome for a number of samples, such as sequencing coverage, DNA copy number, or GC content. This class inherits from both DataFrame and SimpleRleList (one of the AtomicVector types). This means that all of the usual subsetting and applying functions will work. Also, the AtomicList functions, like mean and sum, that automatically apply over the list elements will work. The scalar mathematical AtomicList methods can make this class behave much like a matrix (see Examples).

New objects can be created with the RleDataFrame constructor: RleDataFrame(..., row.names=NULL), where ... can be a list of Rle objects, or one or more individual Rle objects.

Use in Biobase eSet objects

The genoset class defines an annotatedDataFrameFrom method for DataFrame, which makes it possible to include DataFrames as assayData elements. The column names for DataFrame cannot be NULL, which makes it impossible to use them as assays in SummarizedExperiment at this time.

Extends

Class "SimpleRleList", directly. Class "DataFrame", directly.

See Also

DataFrame AtomicList Rle RleList rowMeans colMeans rowSums colSums view-summarization-methods

Examples

showClass("RleDataFrame")

## Constructors
df = new("RleDataFrame", listData=list(A=Rle(c(NA, 2:3, NA, 5), rep(2,
5)), B=Rle(c(6:7, NA, 8:10),c(3,2,1,2,1,1))), nrows=10L)

df2 = RleDataFrame(list(A=Rle(c(NA, 2:3, NA, 5), rep(2, 5)),
B=Rle(c(6:7, NA, 8:10),c(3,2,1,2,1,1))))

df3 = RleDataFrame(A=Rle(c(NA, 2:3, NA, 5), rep(2, 5)), B=Rle(c(6:7,
NA, 8:10),c(3,2,1,2,1,1)))

## AtomicList Methods
runValue(df)
runLength(df)
ranges(df)
mean(df)
sum(df)
df + 5
log2(df) - 1

## Row and Column Summaries
rowSums(df)
colSums(df)
rowMeans(df)
colMeans(df)

## Coercion
as(df, "matrix")
as(df, "list")
as(df, "RleList")
as(df, "DataFrame")
as(df, "data.frame")