getSig: Draw GESs from Reference Database

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

Draw GESs from Reference Database

Description

Functionalities used to draw from reference database (e.g. lincs, lincs_expr) GESs of compound treatment(s) in cell types.

Usage

getSig(cmp, cell, refdb)

getDEGSig(
  cmp,
  cell,
  Nup = NULL,
  Ndown = NULL,
  higher = NULL,
  lower = NULL,
  padj = NULL,
  refdb = "lincs"
)

getSPsubSig(cmp, cell, Nup = 150, Ndown = 150)

Arguments

cmp	character vector representing a list of compound name available in refdb for getSig function, or character(1) indicating a compound name (e.g. vorinostat) for other functions
cell	character(1) or character vector of the same length as cmp argument. It indicates cell type that the compound treated in
refdb	character(1), one of "lincs", "lincs_expr", "cmap", "cmap_expr", or path to the HDF5 file built from build_custom_db function
Nup	integer(1). Number of most up-regulated genes to be subsetted
Ndown	integer(1). Number of most down-regulated genes to be subsetted
higher	numeric(1), the upper threshold of defining DEGs. At least one of 'lower' and 'higher' must be specified. If Nup or Ndown arguments are defined, it will be ignored.
lower	numeric(1), the lower threshold of defining DEGs. At least one of 'lower' and 'higher' must be specified. If Nup or Ndown arguments are defined, it will be ignored.
padj	numeric(1), cutoff of adjusted p-value or false discovery rate (FDR) of defining DEGs if the reference HDF5 database contains the p-value matrix stored in the dataset named as 'padj'. If Nup or Ndown arguments are defined, it will be ignored.

Details

The GES could be genome-wide differential expression profiles (e.g. log2 fold changes or z-scores) or normalized gene expression intensity values depending on the data type of refdb or n top up/down regulated DEGs

Value

matrix representing genome-wide GES of the query compound(s) in cell

a list of up- and down-regulated gene label sets

a numeric matrix with one column representing gene expression values drawn from lincs_expr db of the most up- and down-regulated genes. The genes were subsetted according to z-scores drawn from lincs db.

Examples

refdb <- system.file("extdata", "sample_db.h5", package = "signatureSearch")
vor_sig <- getSig("vorinostat", "SKB", refdb=refdb)
vor_degsig <- getDEGSig(cmp="vorinostat", cell="SKB", Nup=150, Ndown=150,
                        refdb=refdb)
all_expr <- as.matrix(runif(1000, 0, 10), ncol=1)
rownames(all_expr) <- paste0('g', sprintf("%04d", 1:1000))
colnames(all_expr) <- "drug__cell__trt_cp"
de_prof <- as.matrix(rnorm(1000, 0, 3), ncol=1)
rownames(de_prof) <- paste0('g', sprintf("%04d", 1:1000))
colnames(de_prof) <- "drug__cell__trt_cp"
## getSPsubSig internally uses deprof2subexpr function
## sub_expr <- deprof2subexpr(all_expr, de_prof, Nup=150, Ndown=150)

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