get_sig_gsva_categories: Attempt to score the results from simple_gsva()

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Attempt to score the results from simple_gsva()

Description

This function uses a couple of methods to try to get an idea of whether the results from gsva are actually interesting. It does so via the following methods: 1. Use limma on the expressionset returned by simple_gsva(), this might provide an idea of if there are changing signatures among the sample types. 2. Perform a simplified likelihood estimate to get a sense of the significant categories.

Usage

get_sig_gsva_categories(
  gsva_result,
  cutoff = 0.95,
  excel = "excel/gsva_subset.xlsx",
  model_batch = FALSE,
  factor_column = "condition",
  factor = NULL,
  label_size = NULL,
  col_margin = 6,
  row_margin = 12,
  type = "mean"
)

Arguments

gsva_result	Result from simple_gsva()
cutoff	Significance cutoff
excel	Excel file to write the results.
model_batch	Add batch to limma's model.
factor_column	When extracting significance information, use this metadata factor.
factor	Use this metadata factor as the reference.
label_size	Used to make the category names easier to read at the expense of dropping some.
col_margin	Attempt to make heatmaps fit better on the screen with this and...
row_margin	this parameter
type	Either mean or median of the scores to return.

Value

List containing the gsva results, limma results, scores, some plots, etc.

See Also

[score_gsva_likelihoods()] [get_group_gsva_means()] [limma_pairwise()] [simple_gsva()]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.