getSignatureList: Obtain molecular signatures

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Obtain molecular signatures

Description

Retrieves the list of molecular signatures stored in a molecular assay. While getSignatureList() allows to extract signatures of all assays, getGeneSetList(), getMetaboliteSetList() and getProteinSetList() are quick wrappers. But they require assays of specific names/molecular modalities.

Usage

getGeneSetList(object, ..., class = NULL)

getMetaboliteSetList(object, ..., class = NULL)

getProteinSetList(object, ..., class = NULL)

getSignatureList(object, ..., class = NULL, assay_name = activeAssay(object))

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
...	Additional selection helpers from the tidyselect package that match names according to a given pattern.
class	Character vector of signature classes with which to subset the output.
assay_name	Only relevant if the SPATA2 object contains more than one assay: Denotes the assay of interest and thus the molecular modality to use. Defaults to the active assay as set by activateAssay().

Details

These functions retrieve the signatures from the provided object.

• getSignatureList(): The list of signatures from the assay specified in assay_name.

• getGeneSetList(): The list of signatures from the assay with @modality = 'gene' (assay_name = 'gene').

• getMetaboliteSetList(): The list of signatures from the assay with @modality = 'metabolite' (assay_name = 'metabolite').

• getProteinSetLit(): The list of signatures the assay with @modality = 'protein' (assay_name = 'protein').

Value

A named list of character vectors.

See Also

vselect(), lselect()

Documentation of slot @signatures in the MolecularAssay-class. To extract character vectors of molecule names getMolecules() or getGenes(), ... To extract character vectors of signature names getSignatureNames(), getGeneSets(), ... To add signatures addSignature() or addGeneSet(), ...

Examples

library(SPATA2)

object <- loadSpataObject("UKF269T")

## how the different functions work
getAssayNames(object)

# opt 1
activeAssay(object)
gene_sets <- getSignatureList(object)

head(gene_sets)

# opt 2 (equal to opt 1, cause active and only assay is 'gene')
gene_sets <- getSignatureList(object, assay_name = "gene")

head(gene_sets)

# opt 3
gene_sets <- getGeneSetList(object)

head(gene_sets)

# opt 4 - fails cause no 'protein' assay
protein_sets <- getProteinSetList(object)

## using class argument

hm_gene_sets <- getGeneSetList(object, class = "HM")

head(hm_gene_sets)
tail(hm_gene_sets)

two_kinds_of_gene_sets <- getGeneSetList(object, class = c("HM", "RCTM"))

head(two_kinds_of_gene_sets)
tail(two_kinds_of_gene_sets)

# subsetting with tidyselect grammar

tcr_gene_sets <- getGeneSetList(object, contains("TCR"))

str(tcr_gene_sets)

tcr_gene_sets2 <- getGeneSetList(object, contains("TCR") & !starts_with("RCTM"))

str(tcr_gene_sets2)

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.