DetectUTRLengthShift: Detect shifts in 3'UTR length usage between cell populations

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

Detect shifts in 3'UTR length usage between cell populations

Description

Detect global shifts in 3'UTR length usage between defined cell populations. Firsts applies the DUTest function to detect differential usage (DU) peaks on 3'UTRs, after filtering out peaks annotated as proximal to A-rich regions. Identifies peaks on the same 3'UTR as each DU peak, and determines a position of the DU peak on the 3'UTR relative to the terminating exon. Returns a table of DU results, with the location of each peak relative to the total number of peaks on the corresponding 3'UTR. Results table can be input to the PlotUTRLengthShift function to visualise the results, and evaluate global shifts.

Usage

DetectUTRLengthShift(
  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.

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