sc_QC: Quality control of scRNA-seq count data

In YingMa1993/CARD: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

Quality control of scRNA-seq count data

Description

Quality control of scRNA-seq count data

Usage

sc_QC(
  counts_in,
  metaData,
  ct.varname,
  ct.select,
  sample.varname = NULL,
  min.cells = 0,
  min.genes = 0
)

Arguments

counts_in	Raw scRNAseq count data, each column is a cell and each row is a gene.
metaData	data frame, metaData with "ct.varname" specify the cell type annotation information and "sample.varname" specify the sample information
ct.varname	character, the name of the column in metaData that specifies the cell type annotation information
ct.select	vector of cell type names that you are interested in to deconvolute, default as NULL. If NULL, then use all cell types provided by single cell dataset;
sample.varname	character,the name of the column in metaData that specifies the sample information. If NULL, we just use the whole as one sample.
min.cells	numeric, we filtered out the non-expressed cells.
min.genes	numeric we filtered out the non-expressed genes

Value

Return the filtered scRNA-seq data and meta data stored in a S4 class (SingleCellExperiment)

YingMa1993/CARD documentation built on Feb. 14, 2024, 12:24 p.m.