de_stats_selected_pairs: Compute differential expression summary statistics for...

View source: R/de.genes.R

de_stats_selected_pairsR Documentation

Compute differential expression summary statistics for selected pairs of clusters based on de_param().

Description

Compute differential expression summary statistics for selected pairs of clusters based on de_param().

Usage

de_stats_selected_pairs(
  norm.dat,
  cl,
  pairs,
  de.df = NULL,
  de.param = de_param(),
  method = "limma",
  select.genes = NULL,
  mc.cores = 1,
  cl.means = NULL,
  cl.present = NULL
)

Arguments

norm.dat

a normalized data matrix for data.

cl

a cluster factor object.

pairs

A 2-column matrix of cluster pairs.

de.df

Optional. Pre-computed results from de_selected_pairs() using the same pairs. Default = NULL.

de.param

A list of differential gene expression parameters from de_param()

method

If de.df is NULL, use "limma" or "chisq" to compute differentially expressed genes.

mc.cores

If de.df is NULL, number of cores to use for parallel computation.

Value

A list with two objects:

  • de.df A list of results from de_selected_pairs() for each pair.

  • de.genes A list of results from de_stats_pair() for each pair.


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