gsea: Gene Set Enrichment Analysis

In Facottons/DOAGDC: A Package to Download, Organize and Analyze Genomic Data Commons (GDC) Data

Description

Gene Set Enrichment Analysis

Usage

gsea(
  fdr_cutoff = 0.05,
  width = 10,
  height = 3,
  res = 500,
  unit = "in",
  image_format = "png",
  tool = "edgeR",
  id = "geneid",
  pair_name = "G2_over_G1",
  env
)

Arguments

fdr_cutoff	Numerical value indicating the maximum value for FDR values. The default is 0.05.
width	Graphical parameters. See par for more details. As default width = 2000, height = 1500, res = 300 and unit = "px".
height	Graphical parameters. See par for more details. As default width = 2000, height = 1500, res = 300 and unit = "px".
res	Graphical parameters. See par for more details. As default width = 2000, height = 1500, res = 300 and unit = "px".
unit	Graphical parameters. See par for more details. As default width = 2000, height = 1500, res = 300 and unit = "px".
image_format	A character string indicating which image_format will be used. It could be "png" or "svg". The only unit available in "svg" is inches ('in'). The default is "png".
tool	A character string indicating which differential expression analysis tool was last used.
id	A character string indicating which id should be used: "hugo", "gene_symbol", "ensembl" , "refGene" or "geneid". The default is "geneid".
pair_name	A character string indicating which condition name should be used. When there are only two groups the default is "G2_over_G1".
env	A character string containing the environment name that should be used. If none has been set yet, the function will create one in global environment following the standard criteria: 'tumor_data_base_data_type_tumor_data' or 'tumor_data_base_data_type_both_data' (for tumor and not tumor data in separated matrices).

Value

Enriched terms.

Examples

# data already downloaded using the 'download_gdc' function
concatenate_expression("gene",
   name = "HIF3A",
   data_base = "legacy",
   tumor = "CHOL",
   work_dir = "~/Desktop"
)

# separating gene HIF3A expression data patients in two groups
groups_identification_mclust("gene", 2,
   name = "HIF3A",
   modelName = "E",
   env = CHOL_LEGACY_gene_tumor_data,
   tumor = "CHOL"
)

# load not normalized data
concatenate_expression("gene",
   normalization = FALSE,
   name = "HIF3A",
   data_base = "legacy",
   tumor = "CHOL",
   env = CHOL_LEGACY_gene_tumor_data,
   work_dir = "~/Desktop"
)

# start DE analysis
# considering concatenate_expression and groups_identification already runned
dea_edger(
   name = "HIF3A",
   group_gen = "mclust",
   env = CHOL_LEGACY_gene_tumor_data
)

gonto(
   condition = "Upregulated",
   tool = "edgeR", env = CHOL_LEGACY_gene_tumor_data
)

gsea(tool = "edgeR", env = CHOL_LEGACY_gene_tumor_data)

Facottons/DOAGDC documentation built on April 7, 2020, 3:17 a.m.