apply_DEXSeq_test_sce: Apply DEXSeq to detect differential peak usage to a...

View source: R/differential_usage.R

apply_DEXSeq_test_sceR Documentation

Apply DEXSeq to detect differential peak usage to a Single-Cell Experiment object

Description

Apply DEXSeq to detect differential peak usage been select populations. Works by building a 'pseudo-bulk' profile of cell populations by aggregating counts from individual cells into a smaller number of profiles, defined by num.splits.

Usage

apply_DEXSeq_test_sce(
  peaks.sce.object,
  population.1 = NULL,
  population.2 = NULL,
  exp.thresh = 0.1,
  fc.thresh = 0.25,
  adj.pval.thresh = 0.05,
  num.splits = 6,
  seed.use = 1,
  feature.type = c("UTR3", "UTR5", "exon", "intron"),
  replicates.1 = NULL,
  replicates.2 = NULL,
  include.annotations = FALSE,
  filter.pA.stretch = FALSE,
  verbose = TRUE,
  do.MAPlot = FALSE,
  return.dexseq.res = FALSE,
  ncores = 1
)

Arguments

peaks.sce.object

SCE object of peaks

population.1

a target population of cells (can be an ID/cluster label or a set of cell barcode IDs)

population.2

comparison population of cells. If NULL (default), uses all non-population.1 cells

exp.thresh

minimum percent expression threshold (for a population of cells) to include a peak

fc.thresh

threshold for log2 fold-change difference for returned results

adj.pval.thresh

threshold for adjusted P-value for returned results

num.splits

the number of pseudo-bulk profiles to create per identity class (default: 6)

seed.use

seed use

feature.type

genomic feature types to run analysis on (degault: all)

replicates.1

an optional list to define the cells used as replicates for population.1. Will override anything set for the population.1 parameter.

replicates.2

an optional list to define the cells used as replicates for population.2. Will override anything set for the population.2 parameter.

include.annotations

whether to include junction, polyA motif and stretch annotations in output (default: FALSE)

filter.pA.stretch

whether to filter out peaks annotated as proximal to an A-rich region (default: FALSE)

verbose

whether to print outputs (TRUE by default)

do.MAPlot

make an MA plot of results (FALSE by default)

return.dexseq.res

return the raw and unfiltered DEXSeq results object (FALSE by default)

ncores

Number of cores to use for multithreading

Value

a data-frame of results.

Examples


## Not run: 
apply_DEXSeq_test_sce(apa.seurat.object, population.1 = "1", population.2 = "2")

## End(Not run)


VCCRI/Sierra documentation built on July 3, 2023, 6:39 a.m.