results2: Extract and annotate a single DESeq results table

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Extract and annotate a single DESeq results table

Description

Extract and annotate a single contrast. See results_all to annotate all contrasts.

Usage

results2(dds, biomart, exp, ref, trt = "trt", alpha = 0.05, lfcShrink = TRUE)

Arguments

dds	a DESeqDataSet
biomart	annotations from read_biomart with column 1 matching row names in results
exp	name of experimental trt group in the numerator
ref	name of reference trt group in the denominator
trt	treatment group in the design formula
alpha	the significance cutoff for the adjusted p-value cutoff (FDR)
lfcShrink	shrink fold changes using lfcShrink with type = "normal"

Value

A tibble

Author(s)

Chris Stubben

Examples

## Not run: 
library(hciRdata)
res <- results2(pasilla$dds, fly98, "treated", "untreated", trt="condition")

## End(Not run)

HuntsmanCancerInstitute/hciR documentation built on Aug. 20, 2024, 12:22 a.m.