MiRaGE {MiRaGE} | R Documentation

## Inference of Target Gene Regulation via MicroRNA

### Description

Wrapper function computes P-values for target gene regulation via miRNAs.

### Usage

    MiRaGE(gene_exp,location="local",species="MM",ID="refseq",method="mean",test="ks",
    conv="conserved",species_force=T,ID_force=T,conv_force=T)

### Arguments

`gene_exp` | ExpressionSet object which stores target gene expression. featureData must include "gene_id" and phenoData must include "sample_name". The number of columns of expression data MUST be the length of "sample_name". If not, subsetting is required.
`location` | Specify from where tables are retrieved. If location="local", then tables are retrieved from experimental package, "miRNATarget". If location="web", tables are downloaded from MiRaGE Server web site, "http://www.granular.com/DATA/". Default is "local"
`species` | a string specifies target species. This should be either "MM" (mouse) or "HS" (human).Default is "MM".
`ID` | a string specifies gene ID. Default is "refseq".
`method` | a string specifies the treatment of samples. This should be one of "mean", "mixed", or "one_by_one". Default is "mean".
`test` | a string specifies statistical test for P-value computation. This should be one of "ks" (Kolmogorov-Smirnov test), "t" (t-test), or "wilcox" (Wilcoxon test). Default is "ks".
`conv` | a string specifies conservation of miRNA. This should be one of "conserved", "weak_conserve", and "all". Default is "conserved".
`species_force` | a boolean indicating whether target gene table is downloaded (TRUE) or not (FALSE). Default is TRUE.
`ID_force` | a boolean indicating whether gene ID conversion table is downloaded (TRUE) or not (FALSE). Default is TRUE.
`conv_force` | a boolean indicating whether miRNA conservation table is downloaded (TRUE) or not (FALSE). Default is TRUE.

### Details

This wrapper function computes P-values for target gene regulation via miRNAs using the algorithm employed for the MiRaGE server described in Yoshizawa et al (2011). P-values are computed based upon the target gene expression change between two experimental conditions.

### Value

`P0` | data frame. The first column of "P0" contains miRNA names. From the second column to last column includes P-values. Smaller P-values mean that target genes are more likely upregulated in the later sample groups than in the former sample groups
`P1` | data frame. The first column of "P1" contains miRNA names. From the second column to last column includes P-values. Smaller P-values mean that target genes are more likely downregulated in the later sample groups than in the former sample groups

### References

Yoshizawa, M., Taguchi, Y-h., and Yasuda, J. (2011), Inference of Gene Regulation via miRNAs During ES Cell Differentiation Using MiRaGE Method. Int J Mol Sci 12(12):9265-9276

### Examples

    data(gene_exp)
    result <- MiRaGE(gene_exp,species="HS")
    result$P1[1:3,]

[Package MiRaGE version 1.28.0 Index]