perturbTable: Summarise available perturbation data annotations using...

In vitkl/regNETcmap: Tools to study transcriptional regulation using perturbation screens followed by transcriptomic profiling (incl. CMAP, Perturb-seq)

Description

perturbTable Cross Tabulates Connectivity map perturbation data annotations on columns of interest and subsets of perturbations

Usage

perturbTable(CMap_files, formula = pert_type ~ pert_itime,
  pert_ids = NULL, pdata = NULL)

Arguments

CMap_files	a list of directories and urls produced by loadCMap
formula	specify which 2 columns to call table on: pert_type ~ pert_itime or type ~ pert_type to tabulate single column
pert_ids	data.table (optional) a way to select a subset of perturbation data annotations. data.table should be the output of geneName2PerturbAnno or geneID2PerturbAnno (should contain distil_id column, a unique perturbation ID)
pdata	(optional) data.table, the output of openpData. By default perturbTable reads Cmap file (path provided in CMap_files), for multiple test it can be useful to supply data.table.

Value

data.table containing the perturbation details from the Connectivity map project

Author(s)

Vitalii Kleshchevnikov

See Also

openCellInfo, loadCMap, geneName2PerturbAnno

vitkl/regNETcmap documentation built on Feb. 18, 2020, 3:43 a.m.