PA_DEXSeq: Run DEXSeq differential expression on polyA sites

In rnabioco/scrapR: scraps output import and processing in R

Run DEXSeq differential expression on polyA sites

Description

Run DEXSeq differential expression on polyA sites

Usage

PA_DEXSeq(
  mat,
  cell_ids1,
  cell_ids2,
  fc_cut = 0.25,
  padj_cut = 0.1,
  pseudo_n = 4,
  seed = 1,
  type = c("3'UTR"),
  indep_fil = TRUE,
  sep = ";",
  groups1 = NA,
  groups2 = NA
)

Arguments

mat	PA site count matrix
cell_ids1	cell barcodes for group 1
cell_ids2	cell barcodes for group 2
fc_cut	min fold change cutoff
padj_cut	max adjusted p value cutoff
pseudo_n	number of pseudobulk profiles to make for each group
indep_fil	independent filtering for DEXSeq
sep	separator to split and merge names
groups1	vector of grouping for cell_ids1
groups2	vector of grouping for cell_ids2
types	filter to only these types of PA sites, set to NULL to use all

Value

DEXSeq result table

rnabioco/scrapR documentation built on Aug. 14, 2022, 9:38 a.m.