miRhubgeneplot: sort the information to find out the triplets and plot the...

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

Description

This function will sort the information to find out the triplets and plot the top miRNA expression level of modulated ceRNA interaction happened

Usage

miRhubgeneplot(dictionary, mirna_sam, Result_TCGA_LUSC, miRhubgeneoutput,
  w, N)

Arguments

dictionary	miRNA and the corresponding genes' combination in list format, with miRNA name in the first column and the corresponding genes in the second column
mirna_sam	expression data of miRNA in dataframe format, with miRNA's name in rows and sample name in columns
Result_TCGA_LUSC	a list of dataframe formats with miRNA,candidate ceRNAs,and their locations and number of segmentation based on segcluster_peakmerge function.
miRhubgeneoutput	a dataframe formats with miRNA names with the number of bridging ceRNA triplets and the corresponding genes with the number of ceRNA triplets.
w	window size of the each calculation of triplets,the default is 10.
N	number of the samples,the default is 475.

Value

plotp a plot format with miRNA expression in x-axis and the interaction ceRNA in y-axis.

Examples

## Use the internal dataset

data("dictionary", package = "ceRNAmiRNAfun", envir = environment())
data("mirna_sam", package = "ceRNAmiRNAfun", envir = environment())
data("Result_TCGA_LUSC", package = "ceRNAmiRNAfun", envir = environment())
data("miRhubgeneoutput", package = "ceRNAmiRNAfun", envir = environment())

## use miRhubgeneplot to merge out the bridging miRNA and hub genes and then make the plot of the top miRNA expression level of modulated ceRNA interaction happened
miRhubgeneplot(dictionary,mirna_sam,Result_TCGA_LUSC,miRhubgeneoutput,w=10,N=475)
  

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