readCMAPsubset: Read a subsets of perturbations (Connectivity Map data, all...

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

Description

readCMAPsubset uses geneName2PerturbAnno to select all perturbations in a set of cell lines, perturbation types (compound, shRNA, overexpression, e.g.) and time and then uses readCMAP to read Connectivity Map data given these conditions.

Usage

readCMAPsubset(is_touchstone = c("all", T, F)[2],
  pert_types = c("trt_sh.cgs", "trt_oe"), pert_itimes = c("all"),
  cell_ids = c("all"), CMap_files, gene_names = "all",
  keep_one_oe = c("one", "other", "all")[1], landmark_only = F)

Arguments

is_touchstone	logical, select only the perturbation data that is a part of the touchstone dataset (genes profiled across all 9 core cell lines)? Details: https://docs.google.com/document/d/1q2gciWRhVCAAnlvF2iRLuJ7whrGP6QjpsCMq1yWz7dU/
pert_types	a character vector of perturbation types, query for available perturbation types using perturbTable(CMap_files, ~ pert_type)
pert_itimes	a character vector of perturbation times, query for available perturbation times using perturbTable(CMap_files, ~ pert_itime)
cell_ids	a character vector of cell line names, query for available cell line names using perturbTable(CMap_files, ~ cell_id)
CMap_files	a list of directories and urls produced by loadCMap
gene_names	a character vector of HUGO gene names or other valid pert_iname. Use "all" to select all perturbations.
keep_one_oe	keep only one overexpression experiment per gene and condition. Applicable only when pert_types = "trt_oe". Perturbations where sig_id matches pert_id are retained ("one"). To invert the selection use "other". To select all use "all"
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 all knockdown perturbations (3.4GB)
library(regNETcmap)
CMap_files = loadCMap(directory = "../regulatory_networks_by_cmap/data/cmap/")
allIDs = geneName2PerturbAnno(gene_names = "all", CMap_files = CMap_files, is_touchstone = T, pert_types = "trt_sh.cgs")
perturbTable(pdata = allIDs)
CMAP = readCMAP(PerturbAnno = allIDs, CMap_files = CMap_files)
# fast way to read the same data
CMAPsub = readCMAPsubset(is_touchstone = T, pert_types = c("trt_sh.cgs"), pert_itimes = c("all"), cell_ids = c("all"), CMap_files)
perturbTable(pdata = as.data.table(CMAPsub@cdesc))

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