GSEAplots: Execute GSEA Analysis

In kelsiereinaltt/GSEAplot: GSEA Analysis and Plotting Function

Description

Analyzes genetic expression data and determines whether defined gene sets show statistically significant differences with respect to two phenotypes.

Usage

GSEAplots(
  input.ds.name = "",
  input.cls.name = "",
  gene.set.input = "",
  doc.string = "",
  nperm = 1000,
  bar_percent = 0.1,
  gap_percent = 0.1,
  under_percent = 0.1,
  upper_percent = 0.1,
  color_line = "black",
  color_tick = "black",
  abs.val = F
)

Arguments

input.ds.name	Name of the gct expression file.
input.cls.name	Name of the cls phenotype file.
gene.set.input	Name of the geneset file.
doc.string	Name of the output folder for analysis and for naming output files.
nperm	number of permutations.
bar_percent	proportional height of tick mark to window.
gap_percent	proportional height between minimum enrichment score and top of tick mark to the window.
under_percent	proportional height of white space under tick marks to the window size.
upper_percent	proportional height of white space over enrichment graph to the window size.
color_line	color of enrichment score line in plot pdf.
color_tick	color to tick marks on plot.
abs.val	Default is false. Determines whether genes are ranked according to signal to noise or absolute value of signal to noise (when abs.val=T).

Details

GSEA analysis is computed using the Broad Institute's R source code. Genes are ranked according to signal to noise ratio (difference in means/sum of standard deviations for the two phenotypes).

Value

pp - A list pp which includes : plots, gene.set.reference.matrix, gene.set.leading, report1, report2, ES.

plots - A list of ggplot objects, this can act as an input to the function plot.ES() to output a pdf.

gene.set.reference.matrix - A list of each gene set within a gene set database and the gene symbols corresponding to each set.

gene.set.leading - a similar structure to gene.set.reference.matrix but only contains the gene symbols within each gene set that are part of the leading edge set.

report1 - Summary of GSEA analysis data for the first phenotype.

report2 - Summary of GSEA analysis data for the second phenotype.

ES - This object contains the enrichment scores and enrichment tags used to create the plots described earlier. The user can use this information to customize plots as they wish.

References

Subramanian, Tamayo, et al. (2005), PNAS 102, 15545-15550, http://www.broad.mit.edu/gsea/

Examples

 pp = GSEAplots(input.ds.name=expr.input, input.cls.name=pheno.input,
      gene.set.input=gene.set.input, doc.string="GSEA_plots", nperm=1000,
      abs.val=F, bar_percent=0.1, gap_percent=0.1, under_percent=0.1,
      upper_percent=0.1, color_line="black", color_tick="black")

 custom_results= GSEAplots(input.ds.name=expr.input, input.cls.name=pheno.input,
      gene.set.input=gene.set.input, doc.string="custom_results", nperm=1000,
      bar_percent=0.1, gap_percent=0.1, under_percent=0.1, upper_percent=0.1,
      color_line="black", color_tick="black", abs.val=F)

kelsiereinaltt/GSEAplot documentation built on Aug. 9, 2021, 2:58 a.m.