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Mem S4 class, accessors, getters, and setters

Source: R/AllClasses.R, R/methods-Mem.R
Mem-class.Rd

Mem class containing results from multiEnrichMap(), current class version "1.0.0".

Usage

# S4 method for class 'Mem,ANY,ANY,ANY'
x[i, j, k, drop = FALSE]

# S4 method for class 'Mem'
show(object)

Mem_to_list(x, ...)

# S4 method for class 'Mem'
as.list(x)

# S4 method for class 'Mem'
names(x)

# S4 method for class 'Mem'
enrichments(x)

# S4 method for class 'Mem'
enrichments(x) <- value

# S4 method for class 'Mem'
sets(x, ...)

# S4 method for class 'Mem'
sets(x) <- value

# S4 method for class 'Mem'
genes(x, ...)

# S4 method for class 'Mem'
genes(x) <- value

# S4 method for class 'Mem'
geneIM(x, ...)

# S4 method for class 'Mem'
geneIMdirection(x, ...)

# S4 method for class 'Mem'
geneIMdirection(x) <- value

# S4 method for class 'Mem'
geneIMcolors(x, ...)

# S4 method for class 'Mem'
geneIMcolors(x) <- value

# S4 method for class 'Mem'
enrichList(x, ...)

# S4 method for class 'Mem'
enrichIM(x, ...)

# S4 method for class 'Mem'
enrichIMcolors(x, ...)

# S4 method for class 'Mem'
enrichIMcolors(x) <- value

# S4 method for class 'Mem'
enrichIMdirection(x, ...)

# S4 method for class 'Mem'
enrichIMdirection(x) <- value

# S4 method for class 'Mem'
enrichIMgeneCount(x, ...)

# S4 method for class 'Mem'
memIM(x, ...)

# S4 method for class 'Mem'
geneHitIM(x, ...)

# S4 method for class 'Mem'
geneHitIM(x) <- value

# S4 method for class 'Mem'
geneHitList(x, ...)

# S4 method for class 'Mem'
geneHitList(x) <- value

# S4 method for class 'Mem'
headers(x)

# S4 method for class 'Mem'
colorV(x, ...)

# S4 method for class 'Mem'
colorV(x) <- value

# S4 method for class 'Mem'
thresholds(x, ...)

# S4 method for class 'Mem'
thresholds(x) <- value

# S4 method for class 'Mem'
dim(x)

# S4 method for class 'Mem'
dimnames(x)

list_to_Mem(mem)

# S4 method for class 'Mem'
updateObject(object, ..., verbose = FALSE)

# S4 method for class 'Mem'
geneInCategory(x)

# S4 method for class 'Mem'
setsByGene(x)

Arguments

x

Mem object

i

character or integer with gene names

j

character or integer with pathway names

drop

logical always set to FALSE for Mem objects.

...

additional arguments are ignored

value

character vector of names to assign to pathway gene sets

mem

list output from multiEnrichMap()

Value

Mem_to_list() returns a list suitable for other mem functions.

as.list(Mem) returns a list suitable for other mem functions.

names() returns the character vector of enrichment names

enrichments() returns the character vector of enrichment names

sets() returns the character vector of pathway gene sets

list_to_Mem() returns a Mem S4 object, from 'list' or 'Mem' input.

updateObject() returns a Mem S4 object with the current class version, and current valid class definition. It should be able to update any serialized 'Mem' object from previous class versions.

geneInCategory() returns a list named by pathway, containing character vectors with genes in each pathway.

geneInCategory() returns a list named by gene, containing character vectors with associated gene sets.

Functions

  • x[i: Subset a Mem object, Mem[i, j, k], where i are genes, j are pathways, and k are enrichments.

  • show(Mem): Show summary of a Mem object, dimensions defined by genes, sets, enrichments, showing up to 5 entries of each. Also includes a list of analysis parameters: topN, and thresholds.

  • Mem_to_list(): Coerce S4 Mem to legacy list mem format

  • as.list(Mem): Coerce S4 Mem to legacy list mem format

  • names(Mem): Names for the enrichment tests in a Mem object

  • enrichments(Mem): Names for the enrichment tests in a Mem object

  • enrichments(Mem) <- value: Assign names for the enrichment tests in a Mem object

  • sets(Mem): List pathway gene set names in a Mem object

  • sets(Mem) <- value: Assign pathway gene set names to a Mem object

  • genes(Mem): List genes represented

  • genes(Mem) <- value: Assign gene names in a Mem object

  • geneIM(Mem): The gene-enrichment matrix of genes represented in enrichment tests.

  • geneIMdirection(Mem): The matrix of genes tested versus enrichment tests, with directionality.

  • geneIMdirection(Mem) <- value: Assign directional matrix to the gene-enrichment matrix

  • geneIMcolors(Mem): The matrix of colors indicating genes in each enrichment test

  • geneIMcolors(Mem) <- value: Assign a color matrix to the gene-enrichment matrix

  • enrichList(Mem): The list of enrichResult data in an Mem object

  • enrichIM(Mem): The pathway/P-value matrix

  • enrichIMcolors(Mem): The pathway-enrichment directional color matrix

  • enrichIMcolors(Mem) <- value: Assign the pathway-enrichment directional color matrix

  • enrichIMdirection(Mem): The pathway-enrichment directional score matrix

  • enrichIMdirection(Mem) <- value: Assign the pathway-enrichment directional score matrix

  • enrichIMgeneCount(Mem): Pathway-enrichment gene count matrix, genes involved in enrichment of each pathway, for each enrichment test.

  • memIM(Mem): The gene-pathway incidence matrix

  • geneHitIM(Mem): The matrix of genes tested for enrichment, including genes not associated with enrichment results.

  • geneHitIM(Mem) <- value: Assign the matrix of genes tested in a Mem object

  • geneHitList(Mem): The list of genes tested for enrichment, including genes not associated with enrichment results.

  • geneHitList(Mem) <- value: Assign the list of genes tested for enrichment, including genes not associated with enrichment results.

  • headers(Mem): Enrichment data column headers associated to enrichResult data in a Mem object

  • colorV(Mem): List colors assigned to represented

  • colorV(Mem) <- value: Assign colors to enrichments in a Mem object. If supplied 'value' matches the number of 'enrichments(x)', colors are assigned in the order supplied. Otherwise, 'names(value)' must be present in 'enrichments(x)', and values are assigned in matching order.

  • thresholds(Mem): List thresholds defined

  • thresholds(Mem) <- value: thresholds defined in a Mem object. Note that thresholds do not trigger any other updates to the Mem object.

  • dim(Mem): dimensions in order of genes, sets, and enrichments

  • dimnames(Mem): dimension names for each genes, sets, and enrichments

  • list_to_Mem(): Convert legacy list mem format to S4 Mem

  • updateObject(Mem): Confirm Mem object meets current class definition.

  • geneInCategory(Mem): Genes in each pathway set (category)

  • setsByGene(Mem): Pathways gene sets associated with each gene

See also

Other Mem: Mem-data, Mem-slots, check_Mem()

Other jam Mem utilities: MemPlotFolio-class, fixSetLabels(), mem2cnet(), mem2emap()

Examples

# examples for Mem_to_list and as(Mem, "list")
data(Memtest)
mem1 <- Mem_to_list(Memtest)
jamba::sdim(mem1)
#>                   rows cols        class class_v2
#> enrichList           2              list     <NA>
#> enrichLabels         2         character     <NA>
#> colorV               2         character     <NA>
#> geneHitList          2              list     <NA>
#> geneHitIM          203    2       matrix    array
#> memIM               22   16       matrix    array
#> geneIM              22    2       matrix    array
#> enrichIM            16    2       matrix    array
#> multiEnrichDF       16   12   data.frame     <NA>
#> multiEnrichResult   16   14 enrichResult     <NA>
#> thresholds           6              list     <NA>
#> colnames             9              list     <NA>
#> enrichIMcolors      16    2       matrix    array
#> enrichIMdirection   16    2       matrix    array
#> enrichIMgeneCount   16    2       matrix    array
#> geneIMcolors        22    2       matrix    array
#> geneIMdirection     22    2       matrix    array

# list_to_Mem examples
data(Memtest)
mem <- as(Memtest, "list")
Mem <- list_to_Mem(mem)