get_L1000ph2_expression: Retrieve Broad L1000 data from LINCS Phase 2, weighted...

In schurerlab/LINCSanalytics:

Description

Retrieve Broad L1000 data from LINCS Phase 2, weighted average of replicates z-scores

Usage

get_L1000ph2_expression(sig_ids = "all", filter_zscores = "none",
  genes = "all", cells = "all", perturbagens = "all",
  perturbagen_type = "all", perturbagen_dose = "all",
  perturbagen_time = "all", limits = 1000)

Arguments

filter_zscores	string expressing a threshold for specific z-scores retrieval (default "all", admissible ">value" or "<value")
genes	vector of strings with gene names (Default "all")
cells	vector of strings with cell names (Default "all")
perturbagens	vector of strings with perturbagens IDs (Default "all")
perturbagen_type	vector of strings with perturbagen types (Default "all")
perturbagen_dose	numeric vector with perturbagen doses (Default "all")
perturbagen_time	numeric vector with perturbagen times (Default "all")
limits	numeric value, return only the specified number of rows (Default 1000)

Value

data frame containing entity selected and the associated wegthted average z-scores

Examples

get_L1000ph2_expression(genes = c("EGF","RHEB"))
get_L1000ph2_expression(cells = c("MCF7","PC3"),filter_zscores=">2")
get_L1000ph2_expression(cells = c("MCF7","PC3"),filter_zscores=">2")
get_L1000ph2_expression(perturbagens = "BRD-K60230970-001-10-0")

schurerlab/LINCSanalytics documentation built on May 31, 2019, 2:56 p.m.