gsea_squared: #GSEA-squared (last mod. 07/2019 ksheu)

In graeberlab-ucla/glab.library: Data Analysis Functions

#GSEA-squared (last mod. 07/2019 ksheu)

Description

Input: excel file paths for GSEA output, pos and neg enrichment Input: keyword groups to search Output: graph and pvals

Usage

gsea_squared(
  file1,
  file2,
  keywords,
  keyword.labels = keywords,
  keyword_plot_method = 2,
  get.keywords = F,
  dir = getwd(),
  title = ""
)

Arguments

file1, file2	Paths to GSEA excel file outputs
keywords	Keyword groups to evaluate and plot (eg. c("CELL_CYLE", "INFLAMMATORY|IMMUNE"))
keyword.labels	Labels for keyword groups, in the same order (eg. c("cycle", "immune"))
keyword_plot_method	1 = contains, 2 = words start with, 3 = whole word currently only applies to plotting, get.keywords (below) currently only uses whole words
get.keywords	perform ks tests on individual words to get candidate keywords
dir	set output directory

graeberlab-ucla/glab.library documentation built on Oct. 28, 2024, 10:48 a.m.