id_conv_gen {MiRaGE} | R Documentation

## Conversion table between refseq id vs various gene id/probe id generation function

### Description

This function generate id_conv, which describes conversion between refseq gene id vs various gene id/prob id, from the scratch

### Usage

    id_conv_gen(SP="MM",gene_id="all",destdir="./")

### Arguments

`SP` | Species for which gene id conversion table is generated. "MM" for mouse, "HS" for human. Default is "MM"
`gene_id` | gene id for which conversion table toward refseq gene is generated. If "all" is specified, tables for all of available gene ids are generated. Default is "all".
`destdir` | Directory where data sets are saved. Default is "./".

### Details

This function generates gene id conversion table, id_conv, used in the MiRaGE server described in Yoshizawa et al (2011). It saves data frames in the destination directory. The name of data set including each id_conv is the form, "SP_refseq_to_gene_id_id", where SP is either MM or HS and gene_id is gene id defined in biomaRt attributes.

### Note

If the number of empty rows of each id_conv is less than 20000, its usage is strongly discouraged because the resulting P-values are not trusted.

### 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

    ## Not run: id_conv_gen(gene_id="ensembl_transcript_id")

[Package MiRaGE version 1.28.0 Index]