subsetMOCHAObject: 'subsetMOCHAObject'

In MOCHA: Modeling for Single-Cell Open Chromatin Analysis

subsetMOCHAObject

Description

subsetMOCHAObject subsets a tileResults-type object (from callOpenTiles), or a SummarizedExperiment-type object (from getSampleTileMatrix), either by cell type or sample metadata.

Usage

subsetMOCHAObject(
  Object,
  subsetBy,
  groupList,
  removeNA = TRUE,
  subsetPeaks = TRUE,
  verbose = FALSE
)

Arguments

Object	A MultiAssayExperiment or RangedSummarizedExperiment,
subsetBy	The variable to subset by. Can either be 'celltype', or a column from the sample metadata (see 'colData(Object)').
groupList	the list of cell type names or sample-associated data that should be used to subset the Object
removeNA	If TRUE, removes groups in groupList that are NA. If FALSE, keep groups that are NA.
subsetPeaks	If ‘subsetBy' = ’celltype', subset the tile set to tiles only called in those cell types. Default is TRUE.
verbose	Set TRUE to display additional messages. Default is FALSE.

Value

Object the input Object, filtered down to either the cell type or samples desired.

MOCHA documentation built on May 29, 2024, 2:25 a.m.