getSig {signatureSearch} | R Documentation

## 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)

[Package signatureSearch version 1.6.3 Index]