Run differential gene expression analysis

Usage

RunDEGAnalysis(
  exprs,
  group_by,
  ident_1,
  ident_2 = NULL,
  paired_by = NULL,
  meta = "@meta",
  tool = c("DESeq2", "edgeR", "deseq2", "edger"),
  log = get_logger(),
  cache = NULL,
  ncores = 1
)

Arguments

exprs: Expression matrix with genes as rows and samples as columns.
group_by: Column name in meta to group samples for differential expression analysis
ident_1: First identity to compare against
ident_2: Second identity to compare against If not specified, the rest of the samples will be used as the second identity.
paired_by: Column name in meta for paired samples. For example, Subject, for each subject, there should be only one sample in each group (ident_1 and ident_2).
meta: Metadata data frame with sample information. If a Sample column is present, it will be used as the sample identifier, which is the column name in exprs.
tool: Tool to use for differential expression analysis. Currently supports "DESeq2", "edgeR", and "limma".
log: Logger
cache: Directory to store cache files. If NULL, a temporary directory will be used.
ncores: Number of cores to use for parallel processing. If set to 1, the analysis will run in single-threaded mode. If set to a value greater than 1, the analysis will run in multi-threaded mode. This is only applicable for DESeq2.

Value

A data frame with differential expression results. With attributes:

object: The input expression matrix
meta: The metadata used for the analysis
paired_by: The column name used for paired samples, if applicable.
group_by: The column name used for grouping samples.
ident_1: The first identity used for comparison.
ident_2: The second identity used for comparison.