DecoderVariance: Creates a 2d array of variance values calculated across the...

In quon-titative-biology/scAlign: An alignment and integration method for single cell genomics

Description

Creates a 2d array of variance values calculated across the 3rd decoder dimension of a 3d array of decoder matrices. Unless specified, automatically calculates highly variable genes and orders the combined variance matrix in decreasing order, for later graphical analysis analysis.

Usage

DecoderVariance(
  all_data_combined,
  seurat.obj,
  genes.use,
  output.length,
  decreasing = TRUE,
  return.genes = TRUE
)

Arguments

all_data_combined	A 3D matrix of decoder values across conditions, (cells x genes x condition)
seurat.obj	the reference, aligned Seurat object used to correctly populate the rownames of the output array
genes.use	The gene names to use. See ExtractGenes for more information.
output.length	The number of genes to output, important for later graphical analysis.
decreasing	A logical value for ordering the 2nd value of the output list. Setting to TRUE will output genes in order from highest to lowest mean variance.
return.genes	A logical vector defaulted to TRUE. Setting to FALSE will only output the all_data_var, not high_var_genes

Value

A list of arrays, the fist being the variance calculated across decoders, the second a list of order gene indices

See Also

as.SingleCellExperimentList

ExtractGenes

SelectColors

MeanDecoderVariance

GetCharMetadata

quon-titative-biology/scAlign documentation built on Nov. 17, 2021, 9:57 a.m.