gess_fisher {signatureSearch}R Documentation

Fisher Search Method

Description

In its iterative form, Fisher's exact test (Upton, 1992) can be used as Gene Expression Signature (GES) Search to scan GES databases for entries that are similar to a query GES.

Usage

gess_fisher(qSig, higher, lower, chunk_size = 5000, ref_trts = NULL)

Arguments

qSig

qSig object defining the query signature including the GESS method (should be 'Fisher') and the path to the reference database. For details see help of qSig and qSig-class.

higher

The 'higher' threshold. If not 'NULL', genes with a score larger than 'higher' will be included in the gene set with sign +1. At least one of 'lower' and 'higher' must be specified.

lower

The lower threshold. If not 'NULL', genes with a score smaller than 'lower' will be included in the gene set with sign -1. At least one of 'lower' and 'higher' must be specified.

chunk_size

number of database entries to process per iteration to limit memory usage of search.

ref_trts

character vector. If users want to search against a subset of the reference database, they could set ref_trts as a character vector representing column names (treatments) of the subsetted refdb.

Details

When using the Fisher's exact test (Upton, 1992) as GES Search (GESS) method, both the query and the database are composed of gene label sets, such as DEG sets.

Value

gessResult object, the result table contains the search results for each perturbagen in the reference database ranked by their signature similarity to the query.

Column description

Descriptions of the columns specific to the Fisher method are given below. Note, the additional columns, those that are common among the GESS methods, are described in the help file of the gessResult object.

References

Graham J. G. Upton. 1992. Fisher's Exact Test. J. R. Stat. Soc. Ser. A Stat. Soc. 155 (3). [Wiley, Royal Statistical Society]: 395-402. URL: http://www.jstor.org/stable/2982890

See Also

qSig, gessResult, gess

Examples

db_path <- system.file("extdata", "sample_db.h5", 
                       package = "signatureSearch")
# library(SummarizedExperiment); library(HDF5Array)
# sample_db <- SummarizedExperiment(HDF5Array(db_path, name="assay"))
# rownames(sample_db) <- HDF5Array(db_path, name="rownames")
# colnames(sample_db) <- HDF5Array(db_path, name="colnames")
## get "vorinostat__SKB__trt_cp" signature drawn from sample databass
# query_mat <- as.matrix(assay(sample_db[,"vorinostat__SKB__trt_cp"]))
# qsig_fisher <- qSig(query=query_mat, gess_method="Fisher", refdb=db_path)
# fisher <- gess_fisher(qSig=qsig_fisher, higher=1, lower=-1)
# result(fisher)

[Package signatureSearch version 1.0.4 Index]