drug_cell_ranks: Summary ranking statistics across cell types

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

Summary ranking statistics across cell types

Description

The drug_cell_ranks function returns from a gessResult object the ranks of the perturbagens (e.g. drugs) for each cell type. The results are arranged in separate columns of a data.frame. Additionally, it includes in the last columns summary ranking statistics across all cell types, such as min, mean and max values.

Usage

drug_cell_ranks(gessResult)

Arguments

gessResult

'gessResult' object

Value

data.frame

Examples

gr <- gessResult(result=dplyr::tibble(pert=c("p1", "p1", "p2", "p3"),
                                      cell=c("MCF7", "SKB", "MCF7", "SKB"),
                                      type=rep("trt_cp", 4),
                                      NCS=c(1.2, 1, 0.9, 0.6)),
                 query=list(up="a", down="b"), 
                 gess_method="LINCS", refdb="path/to/refdb")
df <- drug_cell_ranks(gr)

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