DAcomp: Compares the gene expression, pathway activation level and...

In martahidalgo/hipathia: HiPathia: High-throughput Pathway Analysis

Compares the gene expression, pathway activation level and the function activation level of the

Description

Compares the gene expression, pathway activation level and the function activation level of the

Usage

DAcomp(
  hidata,
  groups,
  expdes,
  g2 = NULL,
  path.method = "wilcoxon",
  node.method = "limma",
  fun.method = "wilcoxon",
  order = FALSE,
  paired = FALSE,
  adjust = TRUE,
  conf.level = 0.05,
  sel_assay = 1
)

Arguments

hidata	Either a SummarizedExperiment object or a matrix, returned by function hipathia.
groups	Either a character indicating the name of the column in colData including the classes to compare, or a character vector with the class to which each sample belongs. Samples must be ordered as in hidata.
expdes	String, either an equation expression to pas to limma, or the label of the first group to be compared
g2	String, label of the second group to be compared, if not specified in expdes.
path.method	String, method to be used when comparing pathways. Options include wilcoxon (default, performs a Wilcoxon test comparing conditions expdes and g2 - in this case, mandatory parameter) and limma (performs a limma DE analysis using functions lmFit, contrasts.fit and eBayes using the formula in expdes or comparing conditions expdes and g2.
node.method	String, method to be used when comparing nodes. Options include wilcoxon (performs a Wilcoxon test comparing conditions expdes and g2 - in this case, mandatory parameter) and limma (default, performs a limma DE analysis using functions lmFit, contrasts.fit and eBayes using the formula in expdes or comparing conditions expdes and g2.
fun.method	String, method to be used when comparing functions. Options include wilcoxon (default, performs a Wilcoxon test comparing conditions expdes and g2 - in this case, mandatory parameter) and limma (performs a limma DE analysis using functions lmFit, contrasts.fit and eBayes using the formula in expdes or comparing conditions expdes and g2.
order	Boolean, whether to order the results table by the FDRp.value column. Default is FALSE.
paired	Boolean, whether the samples to be compared are paired. If TRUE, function wilcoxsign_test from package coin is used. If FALSE, function wilcox.test from package stats is used.
adjust	Boolean, whether to adjust the p.value with Benjamini-Hochberg FDR method. Default is TRUE.
sel_assay	Character or integer, indicating the assay to be normalized in the SummarizedExperiment. Default is 1.
conf_level	Numeric, cut off for significance. Default is 0.05.

Value

List including comparison results for nodes, pathways and functions, if present.

Examples

data(path_vals)
data(brca_design)
sample_group <- brca_design[colnames(path_vals),"group"]
comp <- DAcomp(path_vals, sample_group, g1 = "Tumor", g2 = "Normal")

martahidalgo/hipathia documentation built on Jan. 12, 2023, 1:44 p.m.