DetectAEU: Find alternative 3' end usage between two single-cell...

In VCCRI/Sierra: PolyA counting and differential transcript usage analysis for scRNA-seq data

Find alternative 3' end usage between two single-cell populations

Description

Wrapper function to DUTest for detecting differential 3' end use. First applies DUTest to test for differential usage between 3'UTRs. For DU 3'UTR peaks, evaluates whether the DU peaks fall in different 3'UTRs.

Usage

DetectAEU(
  peaks.object,
  gtf_gr,
  gtf_TxDb,
  population.1,
  population.2 = NULL,
  exp.thresh = 0.1,
  fc.thresh = 0.25,
  adj.pval.thresh = 0.05,
  num.splits = 6,
  seed.use = 1,
  verbose = TRUE,
  do.MAPlot = FALSE,
  ncores = 1
)

Arguments

peaks.object	Either a Seurat or SCE object of peaks
gtf_gr	GenomicRanges object from a GTF file
gtf_TxDb	TxDb from gtf file
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 to set the randomised assignment of cells to pseudo-bulk profiles
verbose	whether to print outputs (TRUE by default)
do.MAPlot	make an MA plot of results (FALSE by default)
ncores	Number of cores for multithreading

Value

a data-frame of results.

Examples

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

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