import.ace.from.counts: Constructs an 'SingleCellExeriment' object from count matrix,...

In shmohammadi86/ACTIONetExperiment: ACTIONetExperiment container object

Constructs an 'SingleCellExeriment' object from count matrix, gene names, and sample_metadata

Description

Constructs an 'SingleCellExeriment' object from count matrix, gene names, and sample_metadata

Usage

import.ace.from.counts(
  counts_mat,
  feature_metadata = NULL,
  sample_metadata = NULL,
  prefilter = FALSE,
  ...
)

Arguments

counts_mat	Matrix of counts.mat
feature_metadata	Vector or data frame of annotations for features (rows of the count matrix)
sample_metadata	Vector or data frame of annotations for samples (columns of the count matrix)
prefilter	Whether to prefilter genes/cells based on the counts.mat
min.cell.frac.per.gene	Minimum fraction of cells capturing a gene for it to be retained, if prefilter=TRUE (default=0.005)
min.genes.per.cell	Minimum number of required captured genes per cell, if prefilter=TRUE (default=500)

Value

'SingleCellExeriment' object

Examples

ace = import.ace.from.count.matrix(counts.mat.mat, gene_names, prefilter=TRUE)

shmohammadi86/ACTIONetExperiment documentation built on Sept. 13, 2023, 8:55 p.m.