sample_cor_network: Identifying sample-sample correlation network

In zhangjunpeng411/miRsponge: Identification and analysis of miRNA sponge regulation

Identifying sample-sample correlation network

Description

Identifying sample-sample correlation network in terms of sample-specific miRNA sponge networks.

Usage

sample_cor_network(ceRNet, genes_num, method = "Simpson", 
simcutoff = 0.5, padjustvaluecutoff = 0.01, 
padjustmethod = "BH", num.cores = 2)

Arguments

ceRNet	List object, input sample-specific miRNA sponge networks.
genes_num	Number of possible miRNA sponges.
method	Methods for calculating similatiry between two sample-specific miRNA sponge networks, select one of three methods (Simpson, Jaccard and Lin). Default method is Simpson.
simcutoff	A cutoff value of asimilatiry.
padjustvaluecutoff	A cutoff value of adjusted p-values.
padjustmethod	Adjusted method of p-values, can select one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".
num.cores	The number of CPU cores to be selected.

Value

A list of sample-sample correlations.

Author(s)

Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)

References

1. Tucker CM, Cadotte MW, Carvalho SB, et al. A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biol Rev Camb Philos Soc. 2017;92(2):698-715.

2. Jaccard P. The Distribution of the Flora in the Alpine Zone. The New Phytologist 11, no. 2 (1912): 37–50.

3. Lin D, et al. An information-theoretic definition of similarity. In: Icml, vol. 98. 1998. p. 296–304.

Examples

# Obtain expression data file "ExpData.csv" in csv format
ExpDatacsv <- system.file("extdata","ExpData.csv",package="miRspongeR")
ExpData <- read.csv(ExpDatacsv, header=TRUE, sep=",")

# Obtain miRNA-target interaction data file "miR2Target.csv" in csv format
miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR")
miRTarget <- read.csv(miR2Target, header=TRUE, sep=",")

# Identifying sample-specific miRNA sponge interactions, the sppc method 
# is used to identify miRNA sponge interactions
sponge_sample_specific_net <- sponge_sample_specific(miRTarget, ExpData, senscorcutoff = 0.1, method = "sppc")

sample_cor_network_res <- sample_cor_network(sponge_sample_specific_net, 
genes_num = 31, padjustvaluecutoff = 0.05)

zhangjunpeng411/miRsponge documentation built on Aug. 25, 2024, 4:32 p.m.