meanExpr2h5: Calculate Mean Expression Values of LINCS Level 3 Data

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Calculate Mean Expression Values of LINCS Level 3 Data

Description

Function calculates mean expression values for replicated samples of LINCS Level 3 data that have been treated by the same compound in the same cell type at a chosen concentration and treatment time. Usually, the function is used after filtering the Level 3 data with inst_filter. The results (here matrix with mean expression values) are saved to an HDF5 file. The latter is referred to as the 'lincs_expr' database.

Usage

meanExpr2h5(gctx, inst, h5file, chunksize = 2000, overwrite = TRUE)

Arguments

gctx	character(1), path to the LINCS Level 3 gctx file
inst	tibble, LINCS Level 3 instances after filtering for specific concentrations and times
h5file	character(1), path to the destination HDF5 file
chunksize	number of columns of the matrix to be processed at a time to limit memory usage
overwrite	TRUE or FALSE, whether to overwrite or append data to an existing 'h5file'

Value

HDF5 file, representing the lincs_expr database

Examples

gctx <- system.file("extdata", "test_sample_n2x12328.gctx", package="signatureSearch")
h5file <- tempfile(fileext=".h5")
inst <- data.frame(inst_id=c("ASG001_MCF7_24H:BRD-A79768653-001-01-3:10",
                             "CPC012_SKB_24H:BRD-K81418486:10"), 
    pert_cell_factor=c('sirolimus__MCF7__trt_cp', 'vorinostat__SKB__trt_cp'))
meanExpr2h5(gctx, inst, h5file, overwrite=TRUE)

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.