id_conv_gen: Conversion table between refseq id vs various gene id/probe...

In MiRaGE: MiRNA Ranking by Gene Expression

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")

MiRaGE documentation built on Nov. 8, 2020, 8:15 p.m.