getMiRaGEData {MiRaGE} | R Documentation

## Data retrieval function for MiRaGE

### Description

This function retrieves target gene tables of miRNAs, gene id conversion table and miRNA consevation tables

### Usage

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

### Arguments

`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 function retrieves various tables necessary for inference of target gene regulation by miRNAs, based upon the algorithm implemented in the MiRaGE server described in Yoshizawa et al (2011).

### Value

`tb1` | target gene tables of miRNAs. Rownames are miRNA named and colnames are gene ids
`TBL2` | Transposed matrix of tb1. This object is loaded after this function is called.
`conv_id` | Conservation table of miRNAs. It is retrieved only when "conv" is not equal to "all". This object is loaded after this function is called.
`id_conv` | Gene id conversion table between "refseq" ad specified gene id or probe id. This object is loaded after this function is called.

### Note

It is usually called inside the function of "MiRaGE". After the execution of getMiRaGEData, objects listed in value are automatically loaded

### 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

    tb1 <- getMiRaGEData(species="HS")

[Package MiRaGE version 1.28.0 Index]