cross_co_expression: Cross co-expression gene list against differential expression...

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

Description

Cross co-expression gene list against differential expression genes list

Usage

cross_co_expression(
  pair_name = "G2_over_G1",
  final_data,
  width = 2000,
  height = 2000,
  res = 300,
  unit = "px",
  colors = c("green", "blue", "red"),
  venn_diagram_imagetype = "png",
  work_dir,
  fc_cutoff = 2,
  fdr_cutoff = 0.05,
  env
)

Arguments

pair_name	A character string indicating which condition name should be used. When there are only two groups the default is "G2_over_G1".
final_data	A character string indicating the name of which diferential expression package should be used to get the statistical values in the final list. The default is "EBSeq".
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".
colors	A character vector indicating the colors to be used in the venn diagram. The default is c('green', 'blue', "red").
venn_diagram_imagetype	A character string indicating the image_format (e.g. "tiff", "png" or "svg"). The default is "png".
work_dir	A character string specifying the path to work directory.
fc_cutoff	Numerical value indicating the maximum value for Fold Change '(FC). The default is 2.
fdr_cutoff	Numerical value indicating the maximum value for FDR values. The default is 0.05.
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

a list of genes co-expressed and differentially expressed genes inside the determined environment name for further use.

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