GetGroupGeneSet: Extract cluster/group gene sets from MCA

Description Usage Arguments Value Examples

View source: R/group.R

Description

Extract cluster/group gene sets from MCA

Usage

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GetGroupGeneSet(X, group.by, reduction, dims, features, n.features)

## S3 method for class 'Seurat'
GetGroupGeneSet(X, group.by = NULL, reduction = "mca",
  dims = seq(50), features = NULL, n.features = 200)

## S3 method for class 'SingleCellExperiment'
GetGroupGeneSet(X, group.by = NULL,
  reduction = "MCA", dims = seq(50), features = NULL,
  n.features = 200)

Arguments

X

Seurat or SingleCellExperiment object, alternatively a matrix.

group.by

column name of meta.data (Seurat) or ColData (SingleCellExperiment).

reduction

Which dimensionality reduction to use, must be based on MCA.

dims

A vector of integers indicating which dimensions to use with reduction for distance calculation.

features

A character vector of features name to subset feature coordinates for distance calculation.

n.features

A single integer specifying how many top features will be extracted from ranking.

Value

Distance Matrix between groups (column) and genes (row)

Examples

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seuratPbmc <- RunMCA(seuratPbmc, nmcs = 5)
GroupGeneSet <- GetGroupGeneSet(seuratPbmc, dims = 1:5, group.by = "seurat_clusters")

Cortalak/cellID documentation built on Aug. 3, 2020, 9:01 p.m.