RmiR: Coupling miRNA and Gene expression results

In RmiR: Package to work with miRNAs and miRNA targets with R

Description

Coupling miRNA and Gene expression results for a selected target database.

Usage

  RmiR(mirna=NULL,genes=NULL,annotation=NULL,dbname="targetscan",org="Hs",id="probes",id.out="symbol",verbose=FALSE)
  
read.mir(mirna=NULL,genes=NULL,annotation=NULL,id="probes",dbname=c("targetscan","pictar"),org="Hs",at.least=2,id.out="symbol",verbose=FALSE)

Arguments

mirna	A data.frame with two columns, the first with the microRNA names, the second with the expression values.
genes	A data.frame with two columns, the first with gene ID (probes, symbols, ensembl, entrez...), the second with the expression values.
annotation	The annotation package to annotate the genes file with entrez gene ID, eg: Agilent 44k annotation="hgug4112a.db" or annotation="org.Hs.eg.db" for human not using microarrays probes.
dbname	A selected database of miRNA target. See RmiR.hsa_dbconn, default is "targetscan". If using read.mir it can be a vector of databases, default are "targetscan" and "pictar".
id	The type of annotation of the genes input file. An accepted value is one of: "genes" for entrez gene id, "probes" for microarray probes id, "ensembl" for ensembl gene id, "unigene" for unigene gene id and "alias" for official gene symbols and aliases.
id.out	The annotation of the genes in the output. The default it is "symbol", to have the HGNC symbols, it can be also "probes" if the input id is "probes" or "gene" to leave just the entrez gene annotation.
at.least	Minimum number of databases that should yeld the result, when the search is performed in multiple databases with read.mir. If it is 1 it is basically an union between databases. Default is 2.
org	Define the targets database package of the desired organism. Default is "Hs"
verbose	If it is desired or not to have some verbose output while analysing the data. Default is FALSE

Details

RmiR couples the gene expression and microRNA expression. It uses the AnnotationDbi package to annotate the gene expression file. We intend to put already filtered and significant values in the input file, so in case of duplicate probes or different sequences identifying the same gene or more than one values for a miRNA, the function will take just the mean of the different results and give the corresponding coefficent of variation. Each input file must have two columns. The first one for annotation, the second for expression value. The name of the columns does not matter.

read.mir uses RmiR but performs the search in one or more databases and returns only the object present in at.least databases. If at.least is equal to 1 we basically do an union between the results from the databases of choice, if we specify just a database in dbname it is exactly the same of the RmiR function.

Value

mature_miRNA	The resulting miRNAs present in the input file with at least one target in the selected database.
gene_id	The resulting entrez gene ids present in the input file that are also targets in the selected database.
mirExpr	microRNA expression value
geneExpr	Gene expression Value
mirCV	miRNA expression coefficent of variation in case of duplication otherwise is NA
geneCV	Gene expression coefficent of variation in case of duplication otherwise is NA
symbol	If the id.out is "symbol".
probe_id	If the id.out is "probes".

See Also

RmiR.hsa_dbconn,

Examples

  ## Merge gene expression and mirna expression for agilent IDs

  genes <- data.frame(genes=c("A_23_P171258", "A_23_P150053", "A_23_P150053", 
			      "A_23_P150053", "A_23_P202435", "A_24_P90097",
			      "A_23_P127948"))
  genes$expr <- c(1.21, -1.50, -1.34, -1.45, -2.41, -2.32, -3.03)

  mirna <- data.frame(mirna=c("hsa-miR-148b", "hsa-miR-27b", "hsa-miR-25",
			      "hsa-miR-181a", "hsa-miR-27a", "hsa-miR-7",
			      "hsa-miR-32", "hsa-miR-32", "hsa-miR-7"))
  mirna$expr <- c(1.23, 3.52, -2.42, 5.2, 2.2, -1.42, -1.23, -1.20, -1.37)

  RmiR(genes=genes, mirna=mirna, annotation="hgug4112a.db", id="probes")

  ## Search in pictar

  RmiR(genes=genes, mirna=mirna, annotation="hgug4112a.db", id="probes", 
       dbname="pictar")
  ## or

  read.mir(genes=genes, mirna=mirna, annotation="hgug4112a.db", id="probes",
           dbname="pictar", at.least=1)

  ## Search in miranda, pictar and targetscan, present in each database:

  read.mir(genes=genes, mirna=mirna, annotation="hgug4112a.db", id="probes",
	   dbname=c("miranda", "pictar", "targetscan"), at.least=3)

  ## Search in miranda, pictar and targetscan, present in at least 2 database:

  read.mir(genes=genes, mirna=mirna, annotation="hgug4112a.db", id="probes",
	   dbname=c("miranda", "pictar", "targetscan"), at.least=2)
	

RmiR documentation built on Nov. 8, 2020, 5:17 p.m.