GenoGAM (version 1.0.2)

GenomicTiles: GenomicTiles constructor.

Description

This is the constructor function for GenomicTiles. The easiest construction is fropm SummarizedExperiment. However as the class operates on basepair level, the rowRanges are restricted to the GPos class.

Usage

GenomicTiles(assays, chunkSize = 10000, overhangSize = 0, ...)

Arguments

assays

One of two things. Either directly an object of type 'RangedSummarizedExperiment'. Or in case the object is created from raw data, a 'list' or 'SimpleList' of matrix-like elements, or a matrix-like object. All elements of the list must have the same dimensions, and dimension names (if present) must be consistent across elements and with the row names of 'rowRanges' and 'colData'.

chunkSize

An integer specifying the size of one chunk in bp.

overhangSize

An integer specifying the size of the overhang in bp. The overhang is regarded to be symmetric, such that only the overhang of one side should be provided.

...

Further parameters passed to the SummarizedExperiment constructor.

Value

An object of class GenomicTiles.

Details

Most, but not necessary all functionalities of SummarizedExperiment are yet provided.

Examples

## from raw data
gp <- GPos(GRanges(c("chrI", "chrII"), IRanges(c(1,1), c(5,5))))
assay <- matrix(1:10, 10, 1)
gt <- GenomicTiles(assay, chunkSize = 3, rowRanges = gp)

## from SummarizedExperiment
se <- SummarizedExperiment(assay, rowRanges = gp)
gt <- GenomicTiles(se, chunkSize = 3)