# ensembl_liftover

Download and unzip genome liftover file from Ensembl
Recipe source code: https://github.com/rworkflow/ReUseDataRecipe/blob/master/ensembl_liftover.R (opens new window)
Data source: https://ftp.ensembl.org/pub/assembly_mapping/ (opens new window)

# plot

## ensembl_liftover

# Inputs

label type description
species species string 'human' or 'mouse', which maps to the 'homo_sapiens' or 'mus_musculus' folder under source URL
from from string original genome build (case sensitive, must match source URL)
to to string target genome build (case sensitive, must match source URL)

# Outputs

label type description
liftover liftover File[] the unzipped liftover file: ${from}_to_${to}.chain

# Example:

## Get data from evaluting recipe
recipeLoad('ensembl_liftover', return = TRUE)
ensembl_liftover$species <- 'human'
ensembl_liftover$from <- 'GRCh37'
ensembl_liftover$to <- 'GRCh38'
getData(ensembl_liftover, outdir = 'data/folder', notes = c('grch37', 'grch38'))

## Get data from Google bucket directly
dataUpdate('data/folder', cloud=TRUE)
dh <- dataSearch(c('ensembl', 'GRCh37'))
getCloudData(dh[1], outdir = 'data/folder')