runDESeq2: Differential expression analysis with DESeq2

In AlexanderKirchmair/datamisc: Various functions for data handling

Differential expression analysis with DESeq2

Description

Differential expression analysis with DESeq2

Usage

runDESeq2(
  data,
  design = NULL,
  formula = ~1,
  contrasts = NULL,
  lrt_reduced = NULL,
  prefilter = NULL,
  postfilter = NULL,
  min_counts = 5,
  min_samples = 2,
  ctrlgenes = NULL,
  sizefactors = NULL,
  RUV = list(),
  SVA = list(),
  alpha = 0.05,
  ordered = TRUE,
  df = TRUE,
  ncores = NULL,
  shrink = TRUE,
  ihw = TRUE,
  vst = FALSE,
  rlog = FALSE,
  minReplicatesForReplace = 7,
  fitType = "parametric",
  ...
)

Arguments

data	Counts matrix
design	Experimental design/colData
formula	Formula
contrasts	Named list of contrasts, specified as c(factor, level, reflevel)
lrt_reduced	Reduced formula for LRT test
prefilter	Filter before normalization
postfilter	Filter after normalization
min_counts	min_counts in min_samples for filtering
min_samples	min_counts in min_samples for filtering
ctrlgenes	Control genes for normalization (housekeeping genes)
sizefactors	Pre-calculated size factors
RUV	RUV batch effect correction: 'list(empirical = genes, group = column, n = n_vars)'
SVA	SVA batch effect correction: 'list(reduced = formula, n = n_vars)'
alpha	Significance level (default = 0.05)
ordered	Order results (default = TRUE)
df	Return results as data.frame
ncores	Parallel processing
shrink	Use ashr for log2FC shrinkage
ihw	Use independent hypothesis weighting
vst	Add vst-transformed assay
rlog	Add rlog-transformed assay
minReplicatesForReplace	Required number of replicates to replace outliers
fitType	Fit type of dispresion estimate (parametric, local, mean or glmGamPoi)
...	Parameters passed to DESeq

Examples

dds <- DESeq2::makeExampleDESeqDataSet(n = 10000, interceptMean = c(2,5))
dds |> runDESeq2(formula = ~ condition, contrasts = list(BvsA = c("condition", "B", "A")))
dds |> runDESeq2(formula = ~ condition, lrt_reduced = ~ 1)
dds |> runDESeq2(formula = ~ condition, contrasts = list(BvsA = c("condition", "B", "A")), vst = TRUE, ncores = 5)
dds |> runDESeq2(formula = ~ condition, RUV = list(empirical = sample(rownames(dds), 10)), contrasts = list(BvsA = c("condition", "B", "A")))
dds |> runDESeq2(formula = ~ condition, SVA = list(reduced = ~ 1), contrasts = list(BvsA = c("condition", "B", "A")))

AlexanderKirchmair/datamisc documentation built on June 13, 2025, 5:26 a.m.