TFtargetsINcmap: Summarise TF targets enrichment when TF perturbed in...

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

Description

TFtargetsINcmap

Usage

TFtargetsINcmap(regulons, alternative = "less",
  pert_types = c("trt_oe"), cell_ids = c("A375", "A549", "HA1E",
  "HCC515", "HEPG2", "HT29", "MCF7", "PC3"), gene_names = c("NFKB1",
  "E2F1", "MYC", "TP53", "YY1", "JUN", "STAT1", "STAT3"),
  pert_itimes = c("96 h"), CMap_files, keep_one_oe = c("one", "other",
  "all")[1], landmark_only = F, clustermq_memory = 2000,
  clustermq_job_size = 1, min_targets_in_cmap = 3,
  force_gene_names = F)

Arguments

regulons	data.table containing TF regulons (TF and target columns)
alternative	indicates alternative hypothesis for ks.test. "trt_oe": negative_regulator = "less", positive_regulator = "greater"; "trt_sh.cgs" or anything else: negative_regulator = "greater"; positive_regulator = "less"
pert_types	a character vector of perturbation types, query for available perturbation types using perturbTable(CMap_files, ~ pert_type)
cell_ids	a character vector of cell line names, query for available cell line names using perturbTable(CMap_files, ~ cell_id)
gene_names	a character vector of HUGO gene names. Use "all" to select all perturbations.
pert_itimes	a character vector of perturbation times, query for available perturbation times using perturbTable(CMap_files, ~ pert_itime)
CMap_files	a list of directories and urls produced by loadCMap
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	look only at landmark genes. Details: https://docs.google.com/document/d/1q2gciWRhVCAAnlvF2iRLuJ7whrGP6QjpsCMq1yWz7dU/edit
clustermq_memory	When using clustermq: memory requested for each job
clustermq_job_size	When using clustermq: The number of function calls per job
min_targets_in_cmap	minimal number of TF targets in cmap
force_gene_names	look at all gene_names but less cell lines

Value

list containing data.table summary of TF perturbation effects on TF targets, object of class 'GCT' (CMap data), summary of genes vs cell lines available in CMap and returned (gene_cell_counts)

Author(s)

Vitalii Kleshchevnikov

See Also

regFromCMAP, completeCellGeneCombs, showLargestRegulons

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