correlation: Correlation between miRNA and mRNA expression

Description Usage Arguments Value Functions Author(s) References

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

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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:

Functions

Author(s)

Alboukadel Kassambara [email protected]

References

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


kassambara/miRTarget documentation built on May 18, 2017, 4:15 p.m.