deseq2_find_all_markers: Find markers by DESeq2's pairwise wald tests

In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

Find markers by DESeq2's pairwise wald tests

Description

Perform DESeq2's pairwise wald tests, find specifically up or down-regulated markers for each group.

Usage

deseq2_find_all_markers(
  dds,
  grp,
  direction = c("up", "down"),
  design = NULL,
  add.means = !is.null(grp),
  adjust.method = "BH",
  ncore = 1,
  shrunken = TRUE
)

Arguments

dds	DESeqDataSet object.
grp	Vector of sample groups. These must be valid variable names in R and the same length as ncol(object).
direction	Either "up" or "down" or both
design	Design matrix of the experiment, with rows corresponding to samples and columns to coefficients to be estimated.
add.means	Logical indicating if (unweighted) group means per row should be added to the output.
adjust.method	Method used to adjust the p-values for multiple testing. Options, in increasing conservatism, include "none", "BH", "BY", and "holm". See p.adjust for the complete list of options. A NULL value will result in the default adjustment method, which is "BH".
ncore	Number of cores to use.
shrunken	logical, whether to shrink the log fold-change

Value

Data frame.

jdreyf/jdcbioinfo documentation built on Feb. 12, 2025, 4:30 p.m.