results_apeglm: Run all results from a DESeq analysis using apeglm shrinkage

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Run all results from a DESeq analysis using apeglm shrinkage

Description

Run all results from a DESeq analysis using apeglm shrinkage

Usage

results_apeglm(
  object,
  biomart,
  alpha = 0.05,
  subset,
  add_columns,
  trt,
  simplify = TRUE,
  ...
)

Arguments

object	a DESeqDataSet
biomart	annotations from read_biomart with column 1 matching row names in results
alpha	the significance cutoff for the adjusted p-value cutoff (FDR)
subset	sorted index to subset all pairwise comparisons, see check_contrasts for possible contrasts
add_columns	a vector of biomart columns to add to result table, default gene_name, biotype, chromosome, description and human_homolog if present
trt	Compare groups within trt group, default is first term in the design formula
simplify	return a tibble if only 1 contrast present
...	additional options passed to results

Value

A list of tibbles for each contrast

Author(s)

Chris Stubben

Examples

## Not run: 
library(hciRdata)
res <- results_apeglm(pasilla$dds, fly98)
res

## End(Not run)

HuntsmanCancerInstitute/hciR documentation built on March 26, 2024, 3:09 a.m.