import.miRbase.locations: Import the genomic locations of the miRBase precursor...

In drmjc/genomics: Genomics related functions.

Description

Import the genomic locations of the miRBase precursor miRNA's.

Usage

  import.miRbase.locations(gff.file)

Arguments

gff.file

the path to the gff file, avalable from references [1-3]

Value

see import.gff, with 3 additional columns: “ACC”, “ID” and “pos”, eg “MI0006363”, “hsa-mir-1302-2”, “chr1:20229-20366”

Author(s)

Mark Cowley, 2009-01-07

References

[1] ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/genomes/hsa.gff [2] ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/genomes/mmu.gff [3] ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/genomes/rno.gff

Examples

## Not run: 
tmp <- import.miRbase.locations("~/data/miRBase/sequences/12.0/genomes/hsa.gff")
head(tmp)
#         ACC           ID chr     start       end strand score                       pos
# 1 MI0000060 hsa-let-7a-1   9  95978060  95978139      +     .    chr9:95978060-95978139
# 2 MI0000061 hsa-let-7a-2  11 121522440 121522511      -     . chr11:121522440-121522511
# 3 MI0000062 hsa-let-7a-3  22  44887293  44887366      +     .   chr22:44887293-44887366
# 4 MI0000063   hsa-let-7b  22  44888230  44888312      +     .   chr22:44888230-44888312
# 5 MI0000064   hsa-let-7c  21  16834019  16834102      +     .   chr21:16834019-16834102
# 6 MI0000065   hsa-let-7d   9  95980937  95981023      +     .    chr9:95980937-95981023

## End(Not run)

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