rand_query_ES: Generate WTCS Null Distribution with Random Queries

In signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Description

Function computes null distribution of Weighted Connectivity Scores (WTCS) used by the LINCS GESS method for computing nominal P-values.

Usage

rand_query_ES(h5file, N_queries = 1000, dest)

Arguments

h5file	character(1), path to the HDF5 file representing the reference database
N_queries	number of random queries
dest	path to the output file (e.g. "ES_NULL.txt")

Value

File with path assigned to dest

References

Subramanian, A., Narayan, R., Corsello, S. M., Peck, D. D., Natoli, T. E., Lu, X., Golub, T. R. (2017). A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. Cell, 171 (6), 1437-1452.e17. URL: https://doi.org/10.1016/j.cell.2017.10.049

See Also

gess_lincs

Examples

db_path = system.file("extdata", "sample_db.h5", package="signatureSearch")
rand_query_ES(h5file=db_path, N_queries=5, dest="ES_NULL.txt")
unlink("ES_NULL.txt")

signatureSearch documentation built on April 16, 2021, 6 p.m.