meanExpr2h5 | R Documentation |
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.
meanExpr2h5(gctx, inst, h5file, chunksize = 2000, overwrite = TRUE)
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' |
HDF5 file, representing the lincs_expr
database
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)
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