asurat_add_qcmetrics: Compute QC metrics for each sample.

In johannesnicolaus/ASURAT_source: Assisting Interpretable Classifications in Single-cell Transcriptomics

Description

This function computes (i) the number of reads, (ii) number of genes expressed with non-zero read counts, and (iii) percent of reads mapped to the mitochondrial genes.

Usage

asurat_add_qcmetrics(obj, mt_gene_symbol)

Arguments

obj	An ASURAT object.
mt_gene_symbol	A regex pattern to match gene symbols of mitochondrial genes.

Value

An ASURAT object.

Examples

data(cerv_asurat)
cerv <- asurat_make_obj(
  mat_expression = cerv_asurat[["mat_expression"]],
  gene_symbol = cerv_asurat[["gene_symbol"]],
  gene_entrez = cerv_asurat[["gene_entrez"]],
  sample_identity = cerv_asurat[["sample_identity"]]
)
cerv <- qc.addmetrics(obj = cerv, mt_gene_symbol = "^MT-")

johannesnicolaus/ASURAT_source documentation built on Dec. 21, 2021, 2:11 a.m.