readCMAP: Read Connectivity Map data given perturbation annotations

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

Description

readCMAP reads Connectivity Map data given perturbation annotations for a set of HUGO gene names (or Entrez gene ID) including additional filtering by cell line, perturbation type (compound, shRNA, overexpression, e.g.) and time. Details geneName2PerturbAnno

Usage

readCMAP(PerturbAnno, CMap_files, landmark_only = F)

Arguments

PerturbAnno	data.table containing the perturbation details from the Connectivity map project produced by geneName2PerturbAnno
CMap_files	a list of directories and urls produced by loadCMap
landmark_only	read only landmark genes (rows, measured). Details: https://docs.google.com/document/d/1q2gciWRhVCAAnlvF2iRLuJ7whrGP6QjpsCMq1yWz7dU/edit

Value

object of class 'GCT' [package "cmapR"] with 7 slots containing z-score matrix, perturbation and feature details of the Connectivity map project

Author(s)

Vitalii Kleshchevnikov

See Also

openCellInfo, loadCMap, perturbTable

Examples

# read P53 knockdown perturbations
CMap_files = loadCMap(directory = "../regulatory_networks_by_cmap/data/cmap/")
p53IDs = geneName2PerturbAnno(CMap_files = CMap_files, is_touchstone = T, pert_types = "trt_sh.cgs")
CMAP = readCMAP(PerturbAnno = p53IDs, CMap_files = CMap_files)
# read all knockdown perturbations (3.4GB)
allIDs = geneName2PerturbAnno(gene_names = "all", CMap_files = CMap_files, is_touchstone = T, pert_types = "trt_sh.cgs")
CMAP = readCMAP(PerturbAnno = allIDs, CMap_files = CMap_files)

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