assay,RangedRaggedAssay,missing-method {MultiAssayExperiment}R Documentation

Create a Matrix of score values using a GRanges or own ranges (DEFUNCT)

Description

This function can take a GRanges argument and use each range to check for overlaps with any of the current ranges in the first argument and return a score value from the corresponding metadata. This function will only operate on fully disjoint ranges (see isDisjoint for details). It can only work if metadata is present and there is a "score" column in the metadata. Please see example on how to add metadata to a RangedRaggedAssay or GRangesList class. This function uses the overlapsAny function from the GenomicRanges package.

Usage

## S4 method for signature 'RangedRaggedAssay,missing'
assay(x, i, mcolname = "score",
  background = NA, make.names = FALSE, ranges = NULL, type = "any", ...)

Arguments

x

A RangedRaggedAssay or GRangesList class

i

Argument set to missing (not used)

mcolname

A single string indicating the metadata column to use for the values in the resulting assay matrix

background

A default background value for the resulting assay matrix (default NA). This works for non-matching sample and range pairs in the data and will be imputed in the matrix (e.g., 2 for diploid genomes)

make.names

logical (default FALSE) whether to create character format ranges for the rows of the matrix (either from the ranges argument or from the RangedRaggedAssay itself). Example character format: "chr1:2-3:+"

ranges

An optional GRanges object for comparing accross all sample ranges and for superseding the rows for the resulting matrix (default NULL)

type

The type argument from overlapsAny

...

Unused argument

Value

A matrix of values from the score column of the metadata.

See Also

overlapsAny


[Package MultiAssayExperiment version 1.4.9 Index]