getDEGs: Get DEGs from a SE or list of DEA results

In plger/sechm: sechm: Complex Heatmaps from a SummarizedExperiment

Get DEGs from a SE or list of DEA results

Description

Get DEGs from a SE or list of DEA results

Usage

getDEGs(
  x,
  dea = NULL,
  lfc.th = log2(1.3),
  fdr.th = 0.05,
  direction = 0,
  merge = TRUE
)

Arguments

x	A 'SummarizedExperiment' object with DEA results in rowData, or a list of DEA result data.frames.
dea	Which DEA(s) to use (default all). Used only if 'x' is a 'SummarizedExperiment'.
lfc.th	Absolute log-foldchange threshold.
fdr.th	FDR threshold.
direction	If !=0, specifies whether to fetch only upregulated or downregulated features
merge	Logical; whether to take the union of DEGs from the different DEAs (when more than one).

Value

A character vector with the significant features, or a list of such vectors.

Examples

# loading example SE
data("Chen2017", package="sechm")
# this ones doesn't have saved DEAs in the standard format:
getDEGs(Chen2017)

plger/sechm documentation built on Nov. 21, 2023, 8:53 p.m.