inSilicoDb (version 2.8.0)

getDatasetList: Get list of all available dataset identifiers

Description

Get list of all available dataset identifiers that satisfy all specified constraints (see Arguments).

Usage

getDatasetList(...);

Arguments

...

Optional arguments can be passed to the function for more specific requests:

platform

The platform of the chip on which a measurement was done. A platform is identified by its GEO accession code. If specified, only datasets on the given platform are returned.

norm

Type of normalization to use when pre-processing a dataset. Possible values: "ORIGINAL", "FRMA"[1], "SCAN"[2]. If specified, only datasets for which the given preprocessed data is available are returned.

query

If specified, only datasets for which the query keyword appears in either the title or description of the dataset. typical example queries are 'Thyroid Cancer', 'Primary vs Metastasis', 'p53', etc.

curated

If curated = TRUE is specified, only manually curated datasets will be returned.

Value

A list of dataset identifiers.

References

[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.

See Also

Use getDatasetPlatformList for the same functionality with a list of (dataset, platform) tuples as result.

Examples

length(getDatasetList());
## 7167
length(getDatasetList(platform = "GPL570"));
## 2717
length(getDatasetList(platform = "GPL570", norm = "FRMA"));
## 2406
length(getDatasetList(platform = "GPL570", norm = "FRMA", 
                      query = "Thyroid Cancer"));
## 5
getDatasetList(platform = "GPL570", norm = "FRMA", 
               query = "Thyroid Cancer");
## [1] "GSE6004"  "GSE7307"  "GSE32161" "GSE29265" "GSE2109"