GeneStats: Generate gene level global or per group statistics

In minzheguo/SINCERA: An R implementation of SINCERA pipeline for processing single-cell RNA-seq data.

Description

Generate gene level global or per group statistics

Usage

GeneStats(dp, ident, groups = NULL, genes = NULL, min.expression = 1,
  min.gsize = 2, min.avg = 1, stats = c("var", "specificity", "min",
  "max", "avg", "peak1", "peak2", "welch", "ident.fc", "ident.avg", "ident.min",
  "ident.max", "ident.cnt", "ident.pct"))

Arguments

dp	The expression matrix: rows are genes, columns are cells.
ident	A character/factor vector encoding the identities (e.g., cluster, type, sample, condition, etc.) of cells in the expression matrix. The length of the vector should be the same as the number of cells in the expression matrix and the order of cell identities should be the same as the order of cells in the expression matrix.
groups	The identity groups to be included in the calculation.
genes	The set of genes to be included in the calculation; if NULL, will be automatically set to all genes in the expression matrix
min.gsize	The minimum size of a group
min.avg	The minimum of average expression values
stats	A vector containing the statistics to be calculated for each gene, including
min.exp	The threshold vaule of gene expression

Value

A data.frame containing the results

minzheguo/SINCERA documentation built on Feb. 3, 2021, 2:31 p.m.