querymiRTargetbinding: Query miRNA-target interactions by combining expression data...

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

Query miRNA-target interactions by combining expression data and putative miRNA-target interactions

Description

Query miRNA-target interactions by combining expression data and putative miRNA-target interactions.

Usage

querymiRTargetbinding(ExpData, miRTarget, type = c("all", "miRNA", "target"))

Arguments

ExpData	An input gene expression data frame, the rows are samples and the columns are genes.
miRTarget	An input miRNA-target interaction data frame, the first column is miRNA with name "mir" and the second column is target with name "gene".
type	The type of queried miRNA-target interactions, type "all" for querying both miRNAs and targets in gene expression data, type "miRNA" for querying only miRNAs in gene expression data, and type "target" for querying only targets in gene expression data.

Value

A list of queried miRNA-target interactions

Author(s)

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

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=",")
miR2Target_queried <- querymiRTargetbinding(ExpData, miRTarget, type = "all")

zhangjunpeng411/miRspongeR documentation built on Aug. 26, 2024, 6:48 a.m.