Mem class

Mem class containing results from multiEnrichMap().

Usage

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

list_to_Mem(mem)

Mem_to_list(x, ...)

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

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

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

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

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

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

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

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

Arguments

x

Mem object

i

character or integer with gene set / pathway names

j

character or integer with enrichment names

...

additional arguments are ignored

mem

list output from multiEnrichMap()

Value

list_to_Mem() returns a Mem S4 object.

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

Details

Slots

• enrichList: list of enrichResults named by enrichment test.

• enrichLabels: character vector with custom enrichment labels, named by enrichment test.

• colorV: character vector of R colors, named by enrichment test.

• geneHitList: list of vectors named by enrichment test. Vectors are either:
  character vector of genes tested as hits for enrichment, or
  integer vector named by genes with values indicating the directionality, using 1 or -1.

• geneHitIM: numeric matrix with enrichment tests as colnames, and genes as rownames.
  Values are 1 or 0 to indicate gene hits tested,
  optionally 1 or -1 to indicate directionality.

• memIM: numeric matrix with gene sets / pathways as colnames, and genes as rownames.
  Values are 1 or 0 indicating genes present in each pathway.

• geneIM: numeric matrix with enrichment test as colnames, and genes as rownames.
  This matrix differs from 'geneHitIM' in that it only includes genes also in 'memIM', and in that order.

• enrichIM: numeric matrix with enrichment test as colnames, and gene sets / pathways as rownames.
  Matrix values are enrichment P-values, using the appropriate adjusted P-value or FDR to represent significance.

• multiEnrichDF: data.frame with single combined enrichment table.
  Data include union of genes involved in each pathway, and lowest P-value observed across all enrichment tests.

• multiEnrichResult: enrichResult equivalent of 'multiEnrichDF'.
  It is intended to facilitate use in enrichplot functions.

• thresholds: list of thresholds used when calling multiEnrichMap().

• colnames: list to associate actual colnames in 'enrichList' with the conceptual names used in multienrichjam.

• geneIMcolors: character matrix with enrichment test colnames, and gene rownames.
  Values are colors assigned using 'colorV'.

• geneIMdirection: numeric matrix equivalent to 'geneIM' with values 1 and -1 indicating directionality.
  When no directionality is provided, all values will be 1 or 0.

• enrichIMcolors: character matrix with enrichment test colnames, and gene set / pathway rownames.
  Values are color gradients using the appropriate P-value threshold used with multiEnrichMap().

• enrichIMdirection: numeric matrix equivalent to 'enrichIM' with values indicating directional score.
  Directional scores may include a IPA z-score or other directional score where available.
  When not available, all values are 1.

• enrichIMgeneCount: integer matrix equivalent to 'enrichIM'.
  Values are the number of genes involved in the enrichment of each pathway.

Functions

• x[i: Subset a Mem object

• list_to_Mem(): Convert list to Mem S4 object

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

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

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

• geneIM(Mem): The matrix of genes tested versus enrichment tests

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

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

• genes(Mem): List genes represented

• thresholds(Mem): List thresholds defined

• sets(Mem): List gene sets represented

See also

Other Mem: Memtest, check_Mem()

Examples

# See vignettes for a full walk-through

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

# examples for Mem_to_list and as(Mem, "list")
data(Memtest)
mem1 <- Mem_to_list(Memtest)
mem2 <- as(Memtest, "list")
identical(mem1, mem2)
#> [1] TRUE