import.miRbase: Import miRBase records. From the miRBase FTP site ([1]),...

In drmjc/genomics: Genomics related functions.

Description

This function imports the miRNA.xls file, subsets the mir's to those from a particular species, and re-sorts the resulting file. It can also obtain the locations of the miRNA's, either automatically (ie by mirroring the entire ‘sequences/CURRENT’ directory from above FTP site), or by specifying the gff file.

Usage

  import.miRbase(miRNA.xls.file, species.code = "hsa",
    gff = NULL, predict.arm = TRUE)

Arguments

miRNA.xls.file	the path to the miRNA.xls file
species.code	3 letter code such as “hsa”, “mmu”, “rno”
gff	if NULL then method will look for a file called “genomes/<species code>.gff” in the same directory as the miRNA.xls.file; if NULL, then no location info will be inferred; otherwise provide the path to the “<species code>.gff” file
predict.arm	logical: If TRUE, then predict which arm the mature miR exists on (3'/5'). Otherwise set to FALSE.

Author(s)

Mark Cowley, 2009-01-07

References

[1] ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT

drmjc/genomics documentation built on May 15, 2019, 2:22 p.m.