results_all: Extract and annotate all results from a DESeq analysis

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Extract and annotate all results from a DESeq analysis

Description

Extract all possible contrasts and annotate result tables from a DESeq object. Currently supports simple designs with a single variable.

Usage

results_all(
  object,
  biomart,
  vs = "all",
  subset,
  relevel,
  alpha = 0.05,
  add_columns,
  trt,
  lfcShrink = "normal",
  simplify = TRUE,
  ...
)

Arguments

object	a DESeqDataSet
biomart	annotations from read_biomart with column 1 matching row names in results
vs	either compare all vs. all (default) or all vs specific treatment like control, or see note.
subset	index to subset all pairwise comparisons, try combn(sort(samples$trt),2)
relevel	Levels to compare, if missing then levels(dds$trt)
alpha	the significance cutoff for the adjusted p-value cutoff (FDR)
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
lfcShrink	shrink fold changes using lfcShrink, default normal, ashr or none. Use results_apeglm for apeglm shrinkage. The MLE or unshrunken fold change is saved and added to the results as MLE_log2FC
simplify	return a tibble if only 1 contrast present
...	additional options passed to results

Value

A list of tibbles for each contrast

Note

If you combine factors of interest into a single group following section 3.3 in the DESeq2 vignette, you can set vs = "combined" to limit the comparisons. See check_contrasts for details.

Author(s)

Chris Stubben

Examples

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

## End(Not run)

HuntsmanCancerInstitute/hciR documentation built on Dec. 10, 2024, 12:22 p.m.