Description Usage Arguments Details Value Note Author(s) See Also Examples
This function will retrieve a highdimensional dataset for a specific concept of a certain study. It retrieves the data from the server and parses it, converting the high dimensional data to a data.frame.
1 2 3 | getHighdimData(study.name, concept.match = NULL, concept.link = NULL, projection = NULL,
progress.download = .make.progresscallback.download(),
progress.parse = .make.progresscallback.parse())
|
study.name |
a character string giving the name of a study. |
concept.match |
a character string containing the concept name that should be matched. The |
concept.link |
a character string containing the link pointing to the location of the data on the server. Candidate values for this argument can be found in |
projection |
a character string specifying what part of the dataset should be returned: should all data be returned or only a certain type of data, for example only the log values for an mRNA data set. Candidate values can be obtained, see details section on how. (note: the types of data present may differ between studies). |
progress.download |
(The default should be fine for most users) A list of functions that will be called during the download, this allows displaying download progress to the user. The list must contain three items of the following signature:
|
progress.parse |
(The default should be fine for most users) This argument functions identical to |
Retrieving and parsing the data may take some time, depending on the size of the data requested and on your connection characteristics.
A dataframe containing the high dimensional data will only be returned if a projection is specified.
To discover what projections are possible call getHighDimData
, while only providing a study name and concept, i.e. getHighdimData(study.name, concept.match)
or getHighDimData(study.name, concept.link)
.
If a projection is specified, this function returns a list containing the highdimensional data, with the following components:
data |
a dataframe containing the high dimensional data. |
labelToBioMarkerMap |
a hash describing which (column) labels refer to which bioMarker. This component will only be present if biomarker data is available for this particular dataset. See |
If no projection is specified this function returns a list of the projections available for the requested study. No highdimensional data is returned. It will also print the instruction to set the projection argument and a list of the projections that are available.
To be able to access a transmart database, you need to be connected to the server the database is on. If you haven't connected to the server yet, establish a connection using the connectToTransmart
function.
Tim Dorscheidt, Jan Kanis, Rianne Jansen. Contact: development@thehyve.nl
hash, getStudies, getConcepts
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## Not run:
# if a concept contains high dimensional data, use the following command to obtain this data:
getHighdimData(study.name = "GSE8581", concept.match = "Lung")
# you will be told that one of the listed projections needs to be selected:
"No valid projection selected.
Set the projection argument to one of the following options:
default_real_projection
zscore
log_intensity
all_data"
# the following will return the actual data:
data <- getHighdimData(study.name = "GSE8581", concept.match = "Lung", projection = "zscore")
## End(Not run)
|
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