co_expression: Co-Expression Analyses

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

Description

Powered by WGCNA

Usage

co_expression(
  data = NULL,
  name,
  data_base,
  work_dir,
  tumor,
  normalization = TRUE,
  tumor_data = TRUE,
  trait_data = NULL,
  network_type = "unsigned",
  min_module_size = 15,
  max_softpower = 20,
  nthreads = 1,
  me_diss_thres = 0.25,
  width = 2000,
  height = 1500,
  res = 300,
  unit = "px",
  image_format = "png",
  env,
  save_checkpoints = FALSE,
  load_checkpoint = NULL,
  pearson_cutoff = 0.5
)

Arguments

data	Used for external non-log expression data. Matrix or data frame. This data must have patients/sample code as colnames and genes as rownames.
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.
data_base	A character string specifying "GDC" for GDC Data Portal or "legacy" for GDC Legacy Archive.
work_dir	A character string specifying the path to work directory.
tumor	A character string contaning one of the 33 tumors available in the TCGA project. For instance, the "BRCA" stands for breast cancer.
normalization	Logical value where TRUE specify the desire to work with normalized files only. When FALSE, in the second run, do not forget to set env argument. This argument is only applyable to gene and isoform expression data from GDC Legacy Archive. The default is TRUE.
tumor_data	Logical value where TRUE specifies the desire to work with tumor tissue files only. When set to FALSE, it creates two matrices, one containing tumor data and other containing data from not-tumor tissue. The default is TRUE.
trait_data	A character string where "default" indicates that the trait data to be used is provide by the output of check_clinical_terms function. Use "custom" for data inserted by the user after the table2DOAGDC function and with the table object named as trait_data. This object must have patients/sample code as rownames and the trait categories as colnames. By default trait data is not used.
network_type	A character string indicating which network type should be used. WGCNA allows: "unsigned", "signed", and "signed hybrid". The default is "unsigned".
min_module_size	Numerical value specifying the minimum cluster size. The default is 15.
max_softpower	Numerical value indicating the maximum soft thresholding power for which the scale free topology fit indices are to be calculated. The default is 20.
nthreads	Numerical value indicating how many threads to allow. The number of threads should not be more than the number of actual processors/cores. The default is 1.
me_diss_thres	Numerical value specifying the maximum dendrogram cut height for module merging qualified by dissimilarity (i.e., 1-correlation). The default is 0.25.
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".
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).
save_checkpoints	Logical value where TRUE indicates that an external representation of analysis' objects will be saved to file in disk. The default is FALSE.
load_checkpoint	Logical value where TRUE indicates that the saved checkpoint will be loaded and the analysis is going to continue from that point. The default is FALSE.
pearson_cutoff	Numerical value specifying the minimum Pearson correlation value. The default is 0.5.

Value

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

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