filter_spot_enrichments: this function filters the enrichment matrix for interesting...
In tmirus/TTT: What the Package Does (One Line, Title Case)

View source: R/filter_spot_enrichments.R

this function filters the enrichment matrix for interesting terms based on number of spots a term is enriched in and the terms specificity to one cluster

filter_spot_enrichments(
  enrichment.mat,
  term.names,
  clustering = NULL,
  spot.threshold = 10,
  specificity.threshold = 0.75
)

`enrichment.mat`	numeric matrix of spot enrichments containing p-values (GO terms x spots) as produced by test_spot_enrichment()
`term.names`	character vector, full names of GO ids that are the rownames of enrichment.mat
`clustering`	numeric vector assigning each spot (in the same order as in matrix) to a cluster
`spot.threshold`	numeric > 0, number of spots a GO term needs to be enriched in
`specificity.theshold`	numeric, 0<x<1; fraction of spots that a Term is enriched in that need to be in the same cluster for the Term to be deemed interesting

list containing two enries:

enrichment.mat - filtered matrix contining p-values of enrichments test for each spot and GO term (terms x spots)
term.names - character vector containing full names of the GO ids in the enrichment matrix

tmirus/TTT documentation built on April 17, 2021, 11:04 p.m.