Description Usage Arguments Value Functions Author(s) References
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.
1 2 3 4 5 6 7 8  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"))

mir_targets 
an object of class MirTarget containing the miRNAmRNA 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" 
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 pvalue of the correlation test
fdr: Adjusted pvalue 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.
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
Alboukadel Kassambara [email protected]
A. Kassambara. Statistical Tools for Highthroughput Data Analysis. http://www.sthda.com
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.