Relate Deconvolution Subgroups to PROGENy Pathways — compute_subgroups_pathways • multideconv

Computes PROGENy pathway activity from normalized counts and evaluates module relationships between subgroup profiles and pathway activity profiles.

Usage

compute_subgroups_pathways(
  subgroups,
  counts_norm,
  file_name = "Test",
  height = 6,
  width = 12,
  par_mar = c(4, 25, 5, 3),
  pval = 0.05
)

Arguments

subgroups: Output list from compute.deconvolution.analysis().
counts_norm: Normalized expression matrix with genes in rows and samples in columns.
file_name: Prefix used to save output files.
height: Plot height in inches.
width: Plot width in inches.
par_mar: Numeric vector passed to plot margins.
pval: P-value threshold used in module relationship plots.

Value

Invisibly returns NULL; side effects are generated output files.