gess_gcmap {signatureSearch}R Documentation

gCMAP Search Method

Description

Adapts the Gene Expression Signature Search (GESS) method from the gCMAP package (Sandmann et al. 2014) to make it compatible with the database containers and methods defined by signatureSearch. The specific GESS method, called gCMAP, uses as query a rank transformed GES and the reference database is composed of the labels of up and down regulated DEG sets.

Usage

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

Arguments

qSig

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

higher

The 'upper' 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

The Bioconductor gCMAP (Sandmann et al. 2014) package provides access to a related but not identical implementation of the original CMAP algorithm proposed by Lamb et al. (2006). It uses as query a rank transformed GES and the reference database is composed of the labels of up and down regulated DEG sets. This is the opposite situation of the orignal CMAP method from Lamb et al (2006), where the query is composed of the labels of up and down regulated DEGs and the database contains rank transformed GESs.

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 gCMAP 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

Lamb, J., Crawford, E. D., Peck, D., Modell, J. W., Blat, I. C., Wrobel, M. J., Golub, T. R. (2006). The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science, 313 (5795), 1929-1935. URL: https://doi.org/10.1126/science.1132939

Sandmann, T., Kummerfeld, S. K., Gentleman, R., & Bourgon, R. (2014). gCMAP: user-friendly connectivity mapping with R. Bioinformatics , 30 (1), 127-128. URL: https://doi.org/10.1093/bioinformatics/btt592

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_gcmap <- qSig(query=query_mat, gess_method="gCMAP", refdb=db_path)
# gcmap <- gess_gcmap(qsig_gcmap, higher=1, lower=-1)
# result(gcmap)

[Package signatureSearch version 1.0.4 Index]