Description Usage Arguments Value
If only table
and genome
are given, the function will load the data directly into the R workspace. If cachedir
is a path to a directory, this directory will be used to maintain a cache of UCSC tables so they do not need to be re-downloaded on each call. If the data already exists and sync=TRUE
, the function will only re-download and re-extract if the modified dates are different between the cachedir and remote copies. Note that start coordinates in these raw data tables are 0-based, whereas the Goldmine annotation functions will convert these to be 1-based.
1 2 3 |
table |
The UCSC string specific for the table to sync (e.g. "knownGene", "kgXref", etc) |
genome |
The UCSC string specific to the genome to be downloaded (e.g. "hg19", "hg19", "mm10", etc) |
cachedir |
A path to a directory where a cachedir cache of UCSC tables are stored. If equal to |
version |
If "latest" (default) then use the newest version of the table available. If set to a timestamp string of an archived table (format: YYYY-MM-DD-HH-MM-SS), then load this specific version. Obtain these strings by examining the file names under your cache directory. An archive file with a date stamp is saved automatically with each download of a new version. This feature only works if you have a cachedir cache that contains the desired versions. |
sync |
If |
url |
The root of the remote http URL to download UCSC data from (set by default to |
A data.frame or data.table of the desired UCSC table.
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