ceRNA.cor {CeRNASeek} | R Documentation |
identifying miRNA sponge interactions using ceRNA.cor.In this function We implement several popular linear methods ( HyperC, SC) to identify miRNA sponge. interactions.
ceRNA.cor(miRtar, targetce = NULL, geneexp, miRexp, numMIR = 1, method = "pearson", numrandom = 100)
miRtar |
A data frame representing the relationship between miRNA and target. The data frame contains the name of the miRNA and target regulatory relationship.Required option for method "pearson" and "partial correlation". |
targetce |
a character string (vector) specifying candidate target name to analyse (default (targetce = NULL)). |
geneexp |
An input target expression data frame, the columns are genes and the rows are samples.The expression value may be gene expression ,non-coding RNA expression or expression values of circRNAs and so on. Required option for method pearson" and "partial correlation". |
miRexp |
An input miRNA expression data frame, the columns are miRNA and the rows are samples. Required option for method pearson" and "partial correlation". |
numMIR |
a numeric vector that specify the minimum number of 2 gene-shared miRNAs. |
method |
a character string (default "pearson") indicating which statistical method to choose to calculate the ceRNA interaction relationship. One of "pearson" (default), or "partial correlation", can be abbreviated. |
numrandom |
The number of random. Required option for method "partial correlation",default (numrandom = 100). |
Note:All the arguments without default value must be assigned.
A list of identified miRNA sponge interactions containing following components:
ceRNA
predicted 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.
correlation
The correlation of the identified ceRNA interaction relation.
pvalue
The p value of the identified ceRNA interaction relation.
miR_l
Number of miRNAs interacting with each target in the input file.
Paci P , Colombo T , Farina L . Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer[J]. BMC Systems Biology, 2014, 8(1):83. Zhang Y , Xu Y , Feng L , et al. Comprehensive characterization of lncRNA-mRNA related ceRNA network across 12 major cancers[J]. Oncotarget, 2014, 7(39):64148-64167.
##identifying miRNA sponge interactions ##Here we take the regulatory relationship between six genes and 71 miRNAs and corresponding ##expression profilesas an example. ceRNA.cor(miRtar=dataset[["miRtar"]], targetce = NULL, geneexp=dataset[["geneexp"]], miRexp=dataset[["miRexp"]], numMIR = 1,method = "pearson", numrandom = 100)