read_gmql {RGMQL} | R Documentation |
It reads a GMQL dataset, as a folder containing some homogenus samples on disk or as a GRangesList, saving it in Scala memory in a way that can be referenced in R. It is also used to read a repository dataset in case of remote processing.
read_gmql(dataset, parser = "CustomParser", is_local = TRUE, is_GMQL = TRUE) read_GRangesList(samples)
dataset |
folder path for GMQL dataset or dataset name on repository |
parser |
string used to parsing dataset files. The Parsers available are:
Default is CustomParser. |
is_local |
logical value indicating local or remote dataset |
is_GMQL |
logical value indicating GMQL dataset or not |
samples |
GRangesList |
Normally, a GMQL dataset contains an XML schema file that contains name of region attributes. (e.g chr, start, stop, strand) The CustomParser reads this XML schema; if you already know what kind of schema your files have, use one of the parsers defined, without reading any XML schema.
If GRangesList has no metadata: i.e. metadata() is empty, two metadata are generated:
"provider" = "PoliMi"
"application" = "RGMQL"
GMQLDataset object. It contains the value to use as input for the subsequent GMQLDataset method
## This statement initializes and runs the GMQL server for local execution ## and creation of results on disk. Then, with system.file() it defines ## the path to the folder "DATASET" in the subdirectory "example" ## of the package "RGMQL" and opens such folder as a GMQL dataset ## named "data" using CustomParser init_gmql() test_path <- system.file("example", "DATASET", package = "RGMQL") data = read_gmql(test_path) ## This statement opens such folder as a GMQL dataset named "data" using ## "NarrowPeakParser" dataPeak = read_gmql(test_path,"NarrowPeakParser") ## This statement reads a remote public dataset stored into GMQL system ## repository. For a public dataset in a (remote) GMQL repository the ## prefix "public." is needed before dataset name remote_url = "http://www.gmql.eu/gmql-rest/" login_gmql(remote_url) data1 = read_gmql("public.Example_Dataset_1", is_local = FALSE)