CellMix 1.6

Accessing Data in Marker Lists

Description

The S4 generics geneValues and geneValues<- respectively return and set the values associated with each gene in a gene set.

geneIds returns all gene identifiers in a MarkerList object as a standard list.

annotation and annotation<- respectively extract and set the annotation string from a MarkerList object, i.e. the name of Bioconductor annotation package(s) relevant to convert marker identifiers into other IDs.

hasValues tells if a marker list contains numeric values, e.g. specificity scores.

marknames is similar to geneIds but by default returns the all marker names unlisted, i.e. as a character vector.

Usage

geneValues(object, ...)

geneValues(object, ...) <- value

geneIds(object, ...)

geneIds(object) <- value

geneIdType(object)

geneIdType(object, verbose = FALSE) <- value

annotation(object, ...)

annotation(object, ...) <- value

details(object)

incidence(x, ...)

connectivity(object, ...)

nmf(x, rank, method, ...)

S4 (MarkerList,character)
`annotation`(object, ..., check = TRUE) <- value

S4 (MarkerList)
`show`(object)

S4 (MarkerList)
`details`(object)

S4 (MarkerList)
`geneValues`(object, unlist = FALSE)

hasValues(object, ...)

marknames(object, ...)

S4 (vector)
`marknames`(object, simplify = TRUE)

S4 (list)
`marknames`(object, unlist = TRUE, ...)

Arguments

object
an object from/which to get/set data
value
replacement value
...
extra arguments to allow extension. See each method's description for more details.
check
logical that indicates if the validity of the new value should be checked for consistency with the currrent type of identifiers used in the marker list. If TRUE, and the marker list already has associated annotation package(s), then the new annotation package(s) are required to be installed, and the user will be asked for permission to install them if they are not (interactive mode only).
verbose
logical not used.
unlist
a logical that indicates if the values should be returned as a list (FALSE) or as a vector.
simplify
logical that is use when for logical marker lists only, and indicates if all marker names should be returned (simplify=FALSE), or only the ones associated with a TRUE value.
x
target data to fit, i.e. a matrix-like object
rank
specification of the factorization rank. It is usually a single numeric value, but other type of values are possible (e.g. matrix), for which specific methods are implemented. See for example methods nmf,matrix,matrix,ANY. If rank is a numeric vector with more than one element, e.g. a range of ranks, then nmf performs the estimation procedure described in nmfEstimateRank.
method
specification of the NMF algorithm. The most common way of specifying the algorithm is to pass the access key (i.e. a character string) of an algorithm stored in the package's dedicated registry, but methods exists that handle other types of values, such as function or list object. See their descriptions in section Methods. If method is missing the algorithm to use is obtained from the option nmf.getOption('default.algorithm'), unless it can be infer from the type of NMF model to fit, if this later is available from other arguments. Factory fresh default value is ‘brunet’, which corresponds to the standard NMF algorithm from Brunet2004 (see section Algorithms). Cases where the algorithm is inferred from the call are when an NMF model is passed in arguments rank or seed (see description for nmf,matrix,numeric,NULL in section Methods).

Value

a character vector, usually of length 1 but possibly longer.

Methods

  1. annotationsignature(object = "MarkerList"): Extract name of the annotation package from a marker list.

  2. annotationsignature(object = "GEDdata_entry"): annotation gets the name of the annotation package(s) relevant for the data.

  3. annotation<-signature(object = "MarkerList", value = "character"): Sets the name of the annotation package associated to a marker list.

  4. annotation<-signature(object = "MarkerList", value = "NULL"): Reset the annotation package associated to a marker list

  5. connectivitysignature(object = "MarkerList"): Computes the connectivity matrix of each set (i.e. cell/tissue type) of a marker list, i.e. the matrix whose entries are the number of features in common between each pair o cell type.

  6. detailssignature(object = "MarkerList"): Shows more details than the regular show method.

  7. geneIdTypesignature(object = "MarkerList"): Returns the type of gene identifier used in a marker list.

  8. geneIdType<-signature(object = "MarkerList", value = "NULL"): Sets the type of gene identifier used in a marker list to NullIdentifier().

  9. geneIdType<-signature(object = "MarkerList", value = "character"): Sets the type of gene identifier used in a marker list to a given value.

  10. geneIdType<-signature(object = "MarkerList", value = "GeneIdentifierType"): Sets the type of gene identifier associated with a marker list to a given GeneIdentifierType-class object.

  11. geneValuessignature(object = "MarkerList"): Returns the values embedded in a MarkerList object.

  12. incidencesignature(x = "MarkerList"): Computes the incidence matrix of each feature in each set (i.e. cell/tissue type) of a marker list.

    The matrix is computed by converting the MarkerList object into a GeneSetCollection object, for which a method incidence exists in the GSEABase package.

  13. nmfsignature(x = "MatrixData", rank = "MarkerList", method = "ANY"): Calls an NMF algorithm using a MarkerList object, whose length defines the factorization rank. The actual MarkerList object is passed down in argument data.