Datalist_sliding_w: calculate correlation coefficients with ceRNAs of a miRNA by...

In JohnMengChun/ceRNAmiRNAfun: A package of creating an algorithm of identifying microRNA-competing endogenous RNA triplets

Description

This function will calculate correlation coefficients within each window, a sliding mover that contains putative ceRNA triplets composed of a miRNA and several genes, after determining a window size and the number of windows. And the corresponding miRNA expression of each window was the average expression of samples within different windows.

Usage

Datalist_sliding_w(w, dictionary, miRNA_total, mirna_sam, gene_sam)

Arguments

w	window size of the each calculation of triplets,the default is 10.
dictionary	miRNA and the corresponding genes' combinatino in list format, with miRNA name in the first column and the corresponding genes in the second column
miRNA_total	miRNA list in a vector format, the order of miRNA_total should be the same as the first column of dictionary
mirna_sam	expression data of miRNA in dataframe format, with miRNA's name in rows and sample name in columns
gene_sam	expression data of gene in dataframe format, with gene's name in rows and sample name in columns

Value

Realdata a list of dataframe formats with correlation coefficients of genes within each window for each corresponding miRNA average expression.

Examples

## Use the internal dataset

data("dictionary", package = "ceRNAmiRNAfun", envir = environment())
data("miRNA_total", package = "ceRNAmiRNAfun", envir = environment())
data("mirna_sam", package = "ceRNAmiRNAfun", envir = environment())
data("gene_sam", package = "ceRNAmiRNAfun", envir = environment())

## use sliding window to calculate correlations
Datalist_sliding_w(w=10,dictionary,miRNA_total,mirna_sam,gene_sam)

JohnMengChun/ceRNAmiRNAfun documentation built on May 31, 2019, 5:09 p.m.