de_selected_pairs: Perform pairwise differential gene expression tests between...

In AllenInstitute/scrattch.hicat: Hierarchical Iterative Clustering Analysis for Transcriptomic data

Perform pairwise differential gene expression tests between main pairs of clusters in parallel

Description

Perform pairwise differential gene expression tests between main pairs of clusters in parallel

Usage

de_selected_pairs(
  norm.dat,
  cl,
  pairs,
  method = "limma",
  low.th = 1,
  min.cells = 4,
  cl.means = NULL,
  cl.present = NULL,
  use.voom = FALSE,
  counts = NULL,
  mc.cores = 1
)

Arguments

norm.dat	a normalized data matrix for data.
cl	a cluster factor object.
pairs	A 2-column matrix of cluster pairs.
method	Either "limma" or "chisq".
low.th	The minimum expression value used to filter for expressed genes.
cl.present	A matrix of proportions of cells in each cluster with gene detection. Can be generated with get_cl_props(). Default is NULL (will be generated).
use.voom	Logical, whether or not to use voom() for limma calculations. Default is FALSE.
counts	A matrix of raw count data for each cell. Required if use.voom is TRUE. Default is NULL.
mc.cores	A number indicating how many processor cores to use for parallelization.

AllenInstitute/scrattch.hicat documentation built on Oct. 20, 2023, 6:55 a.m.