Description Usage Arguments Value Author(s) See Also Examples
View source: R/readCMAPsubset.R
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.
1 2 3 4 |
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 |
pert_itimes |
a character vector of perturbation times, query for available perturbation times using |
cell_ids |
a character vector of cell line names, query for available cell line names using |
CMap_files |
a list of directories and urls produced by |
gene_names |
a character vector of HUGO gene names or other valid pert_iname. Use |
keep_one_oe |
keep only one overexpression experiment per gene and condition. Applicable only when |
landmark_only |
read only landmark genes (rows, measured). Details: https://docs.google.com/document/d/1q2gciWRhVCAAnlvF2iRLuJ7whrGP6QjpsCMq1yWz7dU/edit |
object of class 'GCT' [package "cmapR"] with 7 slots containing z-score matrix, perturbation and feature details of the Connectivity map project
Vitalii Kleshchevnikov
openCellInfo
, loadCMap
, perturbTable
1 2 3 4 5 6 7 8 9 | # 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))
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