getSig {signatureSearch} | R Documentation |
Functionalities used to draw from reference database (e.g. lincs, lincs_expr) GESs of compound treatment(s) in cell types.
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)
cmp |
character vector representing a list of compound name available
in |
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 |
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 |
lower |
numeric(1), the lower threshold of defining DEGs.
At least one of 'lower' and 'higher' must be specified.
If |
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 |
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
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.
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)