bioconductor-mirtarrnaseq

name

bioconductor-mirtarrnaseq

description

mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. This package utilizes expression or differential expression mRNA and miRNA sequencing results and performs interactive correlation and various GLMs (Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis between mRNA and miRNA expriments. These experiments can be time point experiments, and or condition expriments.

mirTarRnaSeq

Workflows

Mirna Mrna Correlation Multi Timepoint

Identify significant miRNA-mRNA correlations across three or more time points using fold change data and background distribution comparisons.

library(mirTarRnaSeq)

# 1. Parse fold changes and filter mRNAs/miRNAs
mrna <- one2OneRnaMiRNA(mrna_files, pthreshold = 0.05)$foldchanges
mirna <- one2OneRnaMiRNA(mirna_files)$foldchanges

# 2. Calculate Pearson correlation
corr_0 <- corMirnaRna(mrna, mirna, method = "pearson")

# 3. Generate background correlation distribution
outs <- sampCorRnaMirnamrna mirna method   Shrounds   Srounds  


mirRnaDensityCorcorr_0 outs


sig_corrs  threshSigcorr_0 outs pvalue  


miRanda  getInputSpecies threshold  


results  miRandaIntersectsig_corrs outs mrna mirna miRanda
p  mirRnaHeatmapresultscorr upper_bound