dea_edger: Run edgeR gene Differential Expression Analysis (DEA).

Description Usage Arguments Value Examples

View source: R/function_edgeR.R

Description

Run edgeR gene Differential Expression Analysis (DEA).

Usage

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dea_edger(
  name,
  method = "exacttest",
  clinical_pair,
  group_gen,
  fc_cutoff = 2,
  work_dir,
  env,
  fdr_cutoff = 0.05,
  width = 2000,
  height = 1500,
  res = 300,
  unit = "px",
  image_format = "png"
)

Arguments

name

A character string indicating the desired values to be used in next analysis. For instance, "HIF3A" in the legacy gene expression matrix, "mir-1307" in the miRNA quantification matrix, or "HER2" in the protein quantification matrix.

method

A character string indicating which method should be used: "exacttest" or "glmlrt". The default is "exacttest".

clinical_pair

A character string containing one of the group pairs selected after statistical analysis runned in clinical_terms() function.

group_gen

A character string of the groups generation function:

  • "mclust" - groups_identification_mclust();

  • "CoxHR" - groups_identification_coxHR();

  • "clinical"

    groups_identification_clinical().

fc_cutoff

Numerical value indicating the maximum value for Fold Change '(FC). The default is 2.

work_dir

A character string specifying the path to work directory.

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).

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".

Value

A matrix with DE genes in row and statistical values in columns.

Examples

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library(DOAGDC)

# 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
dea_edger(
   name = "HIF3A",
   group_gen = "mclust",
   env = CHOL_LEGACY_gene_tumor_data
)

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