geneName2PerturbAnno: Get Connectivity Map perturbation annotations for genes of...

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

Description

geneName2PerturbAnno retrieves 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

anyGeneID2PerturbAnno retrieves perturbation annotations for a set of gene idenfified using any type of ID in Homo.sapiens or UniProt.ws, including additional filtering by cell line, perturbation type (compound, shRNA, overexpression, e.g.) and time

keep1OE Keep only 1 overexpression experiment per gene and condition. Designed to be applicable to pert_types = "trt_oe".

Usage

geneName2PerturbAnno(gene_names = "TP53", CMap_files,
  is_touchstone = c("all", T, F), pert_types = c("trt_sh.cgs",
  "trt_oe"), pert_itimes = c("all"), cell_ids = c("all"))

anyGeneID2PerturbAnno(keys = "Q9NZL3", CMap_files,
  org.db = c("UniProt.ws", "Homo.sapiens")[1], keytype = "UNIPROTKB",
  is_touchstone = c("all", T, F), pert_types = c("trt_sh.cgs",
  "trt_sh", "trt_sh.css"), pert_itimes = c("all"), cell_ids = c("all"))

keep1OE(PerturbAnno, keep_one_oe = c("one", "other", "all")[1],
  pert_types = "trt_oe", CMap_files)

Arguments

gene_names	a character vector of HUGO gene names or other valid pert_iname. Use "all" to select all perturbations.
CMap_files	a list of directories and urls produced by loadCMap
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)
keys	a character vector of identifiers, check possible options for type of identifier by calling keytypes(org.db)
org.db	org.db of choice: Homo.sapiens or UniProt.ws::UniProt.ws(9606)
keytype	type of identifier used in keys
PerturbAnno	data.table containing the perturbation details from the Connectivity map project produced by geneName2PerturbAnno
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"
pert_types	find duplicates in this perturbation type
CMap_files	a list of directories and urls produced by loadCMap

Details

is_touchstone: A boolean indicating whether the corresponding signature or perturbagen is a member of the Touchstone dataset. Touchstone is a term applied to the subset of CMap perturbagens that are well-annotated and that were systematically profiled across the majority of the core set of 9 cell lines at standardized conditions. Because of these properties Touchstone dataset well-suited as a reference compendium against with to compare external queries.

Value

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

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

data.table containing the perturbation details from the Connectivity map project. Only one overexpression experiment per gene and condition is retained.

Author(s)

Vitalii Kleshchevnikov

Vitalii Kleshchevnikov

Vitalii Kleshchevnikov

See Also

openCellInfo, loadCMap, perturbTable

openCellInfo, loadCMap, perturbTable

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