colocalized-methods: Colocalized features

In Cardinal: A mass spectrometry imaging toolbox for statistical analysis

Description

Find colocalized features in an imaging dataset.

Usage

## S4 method for signature 'MSImagingExperiment,missing'
colocalized(object, mz, ...)

## S4 method for signature 'SparseImagingExperiment,ANY'
colocalized(object, ref, n = 10,
		sort.by = c("correlation", "M1", "M2"),
		threshold = median,
		BPPARAM = getCardinalBPPARAM(), ...)

## S4 method for signature 'SpatialDGMM,ANY'
colocalized(object, ref, n = 10,
		sort.by = c("Mscore", "M1", "M2"),
		threshold = median,
		BPPARAM = getCardinalBPPARAM(), ...)

Arguments

object	An imaging experiment.
mz	An m/z value giving the image to use as a reference.
ref	Either a numeric vector or logical mask of a region-of-interest, or the feature to use as a reference.
n	The number of top-ranked colocalized features to return.
sort.by	The colocalization measure used to rank colocalized features. Possible options include Pearson's correlation ("correlation"), match score ("Mscore"), and Manders' colocalization coefficients ("M1" and "M2").
threshold	A function that returns the cutoff to use for creating logical masks of numeric references.
BPPARAM	An optional instance of BiocParallelParam. See documentation for bplapply.
...	ignored.

Value

A data frame with the colocalized features.

Author(s)

Kylie A. Bemis

See Also

topFeatures

Examples

setCardinalBPPARAM(SerialParam())

set.seed(1)
data <- simulateImage(preset=2, npeaks=10, representation="centroid")

# find features colocalized with first feature
colocalized(data, ref=1)

Cardinal documentation built on Nov. 8, 2020, 11:10 p.m.