build_custom_db: build_custom_db

In yduan004/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

build_custom_db

Description

Build custom reference signature database for GESS methods

Usage

build_custom_db(df, h5file)

Arguments

df

data.frame or matrix containing genome-wide or close to genome-wide GESs of perturbation experiments. The row name slots are expected to contain gene or transcript IDs (e.g. Entrez ids), while the column names are expected to have this structure: '(drug)__(cell)__(factor)', e.g. 'sirolimus__MCF7__trt_cp'. This format is flexible enough to encode most perturbation types of biological samples. For example, gene knockdown or over expression treatments can be specified by assigning the ID of the affected gene to 'drug', and 'ko' or 'ov' to 'factor', respectively. An example for a knockdown treatment would look like this: 'P53__MCF7__ko'.

h5file

character vector of length 1 containing the path to the destination hdf5 file

Details

The perturbation-based gene expression data, here provided as data.frame or matrix, will be stored in an HDF5 file. The latter can be used as reference database by compatible GESS methods of signatureSearch. Various types of pre-processed gene expression data can be used here, such as normalized gene expression intensities (or counts for RNA-Seq); log2 fold changes (LFC), Z-scores or p-values obtained from analysis routines of differentially expressed genes (DEGs).

Value

HDF5 file

Examples

# Generate a data.frame 
df <- data.frame(sirolimus__MCF7__trt_cp=rnorm(1000),
                 vorinostat__SKB__trt_cp=rnorm(1000))
data(targetList)
rownames(df) = names(targetList)
h5file = tempfile(fileext=".h5")
build_custom_db(df, h5file)
library(SummarizedExperiment)
tmp <- SummarizedExperiment(HDF5Array::HDF5Array(h5file, name="assay"))
rownames(tmp) <- HDF5Array::HDF5Array(h5file, name="rownames")
colnames(tmp) <- HDF5Array::HDF5Array(h5file, name="colnames")

yduan004/signatureSearch documentation built on Feb. 19, 2024, 9:30 a.m.