ceRNA.basic {CeRNASeek}

Identifying miRNA sponge interactions using ceRNA.basic function

Description

This function predicts ceRNA interactions by ratio or hypergeometric test.

Usage

ceRNA.basic(miRtar, targetce = NULL, method = "ratio", numMIR = 1,
 cutoff = ifelse(method == "ratio", 1/3, 0.05))

Arguments

miRtar

A data frame representing the relationship between miRNA and target. The data frame contains the name of the miRNA and target regulatory relationship.

targetce

a character string (vector) specifying candidate target name to analyse (default (targetce = NULL)).

method

a character string (default "ratio") indicating which statistical method to choose to calculate the ceRNA interaction relationship. One of "ratio" (default), or "hypergeometric", can be abbreviated.

numMIR

a numeric vector that specify the minimum number of 2 gene-shared miRNAs

cutoff

a numeric vector of the method("ratio","hypergeometric") specifying threshold between ceRNA interactions .(default (1/3)).

Details

Note:All the arguments without default value must be assigned.

Value

A list of identified miRNA sponge interactions containing following components:

• cesig predicted significant triplets and related information,a 5 columns dataframe as following:

  • targetce represented target names,respectively.

  • anotherce names of modulators that another target(modulators) constitutes a ceRNA interaction relation.

  • miRNAs names of miRNA shared by two targets.

  • miRNAs_num number of miRNAs shared by two targets.

  • ratio/pvalue The ratio/pvalue(optional for method("ratio","hypergeometric")) of the identified ceRNA interaction relation.

• cenotsig predicted not significant triplets and related information,a 5 columns dataframe as following:

  • targetce same as targetce in cesig

  • anotherce same as anotherce in cesig

  • miRNAs same as miRNAs in cesig

  • miRNAs_num same as miRNAs_num in cesig

  • pvalue same as pvalue in cesig

References

Xu J , Feng L , Han Z , et al. Extensive ceRNA–ceRNA interaction networks mediated by miRNAs regulate development in multiple rhesus tissues[J]. Nucleic Acids Research, 2016:gkw587.

Examples

##identifying miRNA sponge interactions
##Here we take six candidate targets(modulators) for example
ceRNA.basic(miRtar=dataset[["miRtar"]],targetce=NULL,method="ratio",numMIR = 1,cutoff =1/3)