Description Usage Arguments Details References See Also Examples
Get information about the availability and the default parameters of a dataset.
1 | getDatasetInfo(dataset, platform, ...);
|
dataset |
Valid dataset identifier: the GEO or InSilico DB accession code. |
platform |
The platform of the chip on which a measurement was done. A platform is identified by its GEO accession code. |
... |
Optional arguments can be passed to the function for more specific requests:
|
The function getDatasetInfo
has two functionalities.
Its first functionality is to return the default parameters of the given dataset if it is called with dataset and platform as only arguments.
Its second functionality is to check the availability of a dataset when optional arguments are specified. Do not forget to surround the function call by a tryCatch
function when checking for availability.
[1] MN. McCall, BM. Bolstad, and RA. Irizarry, Frozen Robust Multi-Array Analysis (fRMA), Biostatistics, vol. 11, no. 2, pp. 242-253 , 2008.
[2] SR. Piccolo, Y. Sun, JD. Campbell, ME. Lenburg, AH. Bild, and WE. Johnson, A single-sample microarray normalization method to facilitate personalized-medicine workflows, Genomics, vol. 100, no. 6, pp. 337-344, 2012.
Is automatically called before getDataset
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | InSilicoLogin("rpackage_tester@insilicodb.com", "5c4d0b231e5cba4a0bc54783b385cc9a");
data.id <- "GSE781";
plt.id <- "GPL96";
## return the default parameters when calling getDataset
eset <- getDatasetInfo( data.id, plt.id);
eset$norm;
## [1] "FRMA"
plt.id <- "GPL97";
## check the availability of the normalizations
norms <- c("FRMA", "ORIGINAL")
output <- sapply(norms, function(n) {
tryCatch({
eset <- getDatasetInfo(data.id, plt.id, norm = n);
eset$norm;
}, error = function(e) {
message(e);
});
});
output$FRMA
## NULL
output$ORIGINAL
## [1] "ORIGINAL"
|
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