correlation: Correlation between miRNA and mRNA expression

In kassambara/miRTarget: Find miRNA targets

Description

Compute the correlation between the expression of each miRNA and its potential mRNA targets. If a gene is targeted by a miRNA we expect that the expression profile of the gene and the miRNA are anticorrelated.

Usage

corr_mir_mrna(mir_targets, mir_mrna_exprs, mirs_of_interest = "all",
  method = "pearson", stand = TRUE, sortby = c("cor.coeff", "p.value",
  "fdr", "none"), show_progress = TRUE)

viz_mrna_per_mir(object, coeff = 0.5, lab.size = 8, lab.angle = 45,
  output = c("plot", "table"))

viz_neg_cor_fraction(object, output = c("plot", "table"))

Arguments

mir_targets	an object of class MirTarget containing the miRNA-mRNA target interactions. It must contains three columns: mirna_name | target.gene_name | status.
mir_mrna_exprs	an object of class MirMrnaExprs, as generated by the function combine_mir_mrna_exprs(). It must contains the expression of miRNAs and mRNAs.
mirs_of_interest	a vector containing the names of miRNA for which you want to compute correlation analysis against target genes. Default value is "all".
method	method to be used for correlation analyses. Allowed values are one of "pearson", "kendall", or "spearman.
stand	logical value. If TRUE the miR/mRNA expression data are standardized before computing correlation. Default value is TRUE.
sortby	Specify how to sort the result. Allowed values are one of "cor.coeff", "p.value", "fdr", or "none": Abbreviation is allowed. Default value is "cor.coeff".
show_progress	logical value. If TRUE, a progress bar is shown.
object	an object of class CorMirTarget as generated using
coeff	correlation coefficient threshold. miRNAs having absolute
lab.size	size of x axis labels
lab.angle	rotation angle of x axis labels correlation >= coeff with one or more mRNAs are kept.
output	allowed values are "plot" or "table"

Value

Returns an object of class CorMirTargets which is a data.frame containing correlation between miRNAs and their mRNAs. Column names of the results are as follow:

• mirna_name: Name of miRNAs

• target.gene_name: The name of target genes

• cor.coeff: Correlation coefficient

• p.value: The p-value of the correlation test

• fdr: Adjusted p-value using BH multiple testing correlation. This calculated separatly for the targets of each miRNA.

• status: miRNA Target status. P for predicted, V for validated; PV for predicted and validated.

Functions

• corr_mir_mrna: Compute correlation between miRNA and mRNA expression

• viz_mrna_per_mir: Visualize the number of correlated mRNAs per miRNA

• viz_neg_cor_fraction: Fraction of negative correlation events

Author(s)

Alboukadel Kassambara [e-mail]

References

A. Kassambara. Statistical Tools for High-throughput Data Analysis. http://www.sthda.com

kassambara/miRTarget documentation built on May 20, 2019, 7:40 a.m.