CellMix 1.6

Enhanced Subsetting for Matrix-like Data

Description

These methods subset Matrix-like data only keeping rows whose names are in common with some other data.

Usage

S4 (MatrixData,logical)
`intersect`(x, y)

S4 (MatrixData,character)
`intersect`(x, y)

S4 (MatrixData,MatrixData)
`intersect`(x, y)

S4 (MatrixData,MarkerList)
`intersect`(x, y)

Arguments

x
vectors (of the same mode) containing a sequence of items (conceptually) with no duplicated values.
y
vectors (of the same mode) containing a sequence of items (conceptually) with no duplicated values.

Details

The generic for these methods is taken from the GSEABase package because it is entirely imported by CellMix. However, a more natural definition would be to be able to use the -- currently conflicting -- version defined in the recommended BiocGenerics package.

Methods

  1. intersectsignature(x = "MatrixData", y = "logical"): This method is equivalent to subset(x, y).

  2. intersectsignature(x = "MatrixData", y = "character"): Subset a matrix-like object by only keeping the rows whose names are in a given reference character vector.

  3. intersectsignature(x = "MatrixData", y = "MatrixData"): Subset a matrix-like object by only keeping the rows whose names are in common with another matrix-like data.

    This is a shortcut for intersect(x, featureNames(y), ...).

  4. intersectsignature(x = "MatrixData", y = "MarkerList"): Subset a matrix-like object by only keeping the features in common with a MarkerList object. Note that no ID conversion is attempted, meaning that marker IDs must match exactly feature names used in the matrix data.

    This is a shortcut for intersect(x, featureNames(y), ...).