setShared: Get the overlap between sets

In Solatar/setR:

Description

Imports: data.table purrr ggplotify reshape2 AnnotationDbi org.Hs.eg.db org.Mm.eg.db plotly

Usage

setShared(
  sets,
  minOverlap = 2,
  Species = NA,
  IDfrom = "SYMBOL",
  IDto = "SYMBOL",
  HMstats = T,
  HMlabels = 24,
  plotly = F
)

Arguments

sets	list, each item (i.e. a set) is a vector of strings
minOverlap	integer, indicating the minimum number of sets in which genes should show up
Species	string, either "Homo sapiens" or "Mus musculus", indicating the species the set items refer to
IDfrom	string, anything valid in mapIds (e.g. 'ENTREZID' or 'SYMBOL'), indicating the input ID type of set items
IDto	string, anything valid in mapIds (e.g. 'ENTREZID' or 'SYMBOL'), indicating the output ID type of set items
HMstats	boolean, should overlap percentage be shown in the tiles?
HMlabels	boolean, should x and y axis have text, i.e. sample names
plotly	boolean, should a plotly graph be shown instead of ggplot?

Value

a list: two ggplot objects (venn & heatmap), a vector of overlapping genes and a boolean table with all genes

Examples

IDs1 <- setRead("up", path=myPath1)
IDs2 <- setRead("up", path=myPath2)
set1 <- setMake("mySet", IDs1, "Homo sapiens")
set2 <- setMake("mySet", IDs2, "Homo sapiens")
setSave(list(set1, set2), myFolder)

Solatar/setR documentation built on Dec. 5, 2020, 10:50 p.m.