GetGroupGeneRanking: Gene Specificity Ranking Calculation

Description Usage Arguments Value Examples

View source: R/group.R

Description

Gene Specificity Ranking Calculation

Usage

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GetGroupGeneRanking(X, group.by, reduction, dims, features)

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

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

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 embeddings and loadings for distance calculation.

features

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

Value

List of genes ranking for each groups

Examples

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

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