all_steps_interface: A function for conducting the algorithm through the toy data

In ywhsiao/ceRNAR: ceRNAR: An R Package for Identification and Analysis of ceRNAs-miRNA Triplets

A function for conducting the algorithm through the toy data

Description

A function to allow users to conducting the

Usage

All_steps_interface(
  path_prefix = NULL,
  project_name = "demo",
  disease_name = "DLBC",
  gene_exp = gene_exp,
  mirna_exp = mirna_exp,
  surv_data = surv_data,
  filtering = "less",
  window_size = 10,
  cor_method = "pearson",
  cor_threshold_peak = 0.85
)

Arguments

path_prefix	user's working directory
project_name	the project name that users can assign (default: demo)
disease_name	the abbreviation of disease that users are interested in (default: DLBC)
gene_exp	location of gene expression data (default: gene_exp)
mirna_exp	location of miRNA expression data (default: mirna_exp)
surv_data	location of survival data (default: surv_data)
filtering	three different filtering criteria, including strict, moderate and less. (Default: less)
window_size	the number of samples for each window (default:10)
cor_method	selection of correlation methods, including pearson and spearman (default: pearson)
cor_threshold_peak	peak threshold of correlation value between 0 and 1 (default: 0.85)

Value

a dataframe object

Examples

data(gene_exp)
data(mirna_exp)
data(surv_data)
All_steps_interface(
path_prefix = NULL,
project_name = 'demo',
disease_name = 'DLBC',
gene_exp = gene_exp,
mirna_exp = mirna_exp,
surv_data = surv_data,
filtering = 'less',
window_size = 10,
cor_method = 'pearson',
cor_threshold_peak = 0.85)

ywhsiao/ceRNAR documentation built on Aug. 6, 2023, 3:13 p.m.