combineGroupings-methods: description of function combineGroupings

In stela2502/BioData: The package allows to annotate a numeric data.table with col and row data

Description

combine different grouping informations to create overlaps. Implemented to combine different subset RFclusterings into one including all features.

Usage

combineGroupings(
  x,
  colGroups,
  new_name = "Merged Group 1",
  minCellOverlap = 5,
  minGroupOverlap = length(colGroups) - 2,
  minCellsInReturnGroup = NULL
)

Arguments

x	The BioData object
colGroups	which groupings to combine (samples columns)
new_name	the name of the new grouping (default="Merged Group 1" will replace existing information)
minCellOverlap	while calculating the grouing overlap - how many cells need to overlap with each other default=5
minGroupOverlap	while caulculating the overlap - how many groups should overlap in order to considder a cell overlapping default=length(colGroups)-2
minCellsInReturnGroup	merge all groups with less than this number of cells into a ungrouped group default=1% of the bigges sname subgroup

Details

This function will calculate the overlap in group names for each cell to all other cells,

select the cells that match the requirement ( minCellOverlap and minGroupOverlap) and asigne the group id of the biggest group

to this cell.

The same algorythm will be applied for all cells that end up in small groups before the final ungrouped cells are assigned.

Examples

combineGroupings(BioDataObj, colnames(BioDataObject$samples)[1:10], 
minCellOverlap = 5, minGroupOverlap = 8, minCellsInReturnGroup = 20)

stela2502/BioData documentation built on Feb. 23, 2022, 5:47 a.m.