GSEAplots: Execute GSEA Analysis

In kelsiereinaltt/GSEApackage: 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,
  fdr.q.val.threshold = 0.25, 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, gs.size.threshold.max = 1000)

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
fdr.q.val.threshold	significance threshold for fdr q-values
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)
gs.size.threshold.max	Default is 1000. Maximum matches between geneset and gene labels

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/

kelsiereinaltt/GSEApackage documentation built on May 27, 2020, 12:05 a.m.