Mem description of slots

Mem description of slots, for reference, slots may change at any time

Details

Note that the Mem S4 object is intended to be used via the accessor functions as described in Mem-class.

However, for reference, and in case really necessary the slots are described in more detail below. These slots may change at any time, as the 'Mem' S4 object evolves after more usage, so relying upon specific slots to be stable may not be ideal.

The descriptions below should be edited whenever the 'Mem' S4 slot structure changes, but be prepared there may sometimes be some delay even under the best of intentions.

Enrichment data input

enrichList: list of enrichResults named by enrichment test. This list represents the input enrichment data.
enrichLabels: character vector with custom enrichment labels, 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.

Incidence matrix data

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.

Combined enrichment data

Enrichment data are combined into singular objects, mainly intended to be used with clusterProfiler related functions. Also the data.frame could be used as a supplemental table.

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.

Analysis details

colorV: character vector of R colors, named by enrichment test.
thresholds: list of thresholds used when calling multiEnrichMap().
- p_cutoff: numeric P-value threshold for significant enrichment.
- min_count: integer number of genes involved in a pathway for the pathway to be considered significant.
headers: list to associate actual colnames (headers) in 'enrichList' with the conceptual names used in multienrichjam.

Additional incidence matrix data

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.