get_gcp_expression: Retrieve Broad Global Chromatin Profiling (GCP) data, plate...

In schurerlab/LINCSanalytics:

Description

Retrieve Broad Global Chromatin Profiling (GCP) data, plate normalized log2 fold change.

Usage

get_gcp_expression(filter_foldchange = "none", histone_modification = "all",
  cells = "all", perturbagens = "all", perturbagen_dose = "all",
  replicates = "all", limits = 1000)

Arguments

filter_foldchange	string expressing a threshold for specific log2 fold change retrieval (default "all", admissible ">value" or "<value")
histone_modification	vector of strings with histone modifications (Default "all")
cells	vector of strings with cell names (Default "all")
perturbagens	vector of strings with perturbagens IDs (Default "all")
perturbagen_dose	numeric vector with perturbagen doses (Default "all")
replicates	string, return each replicate separately (Default "all") or aggregated as averge value (using replicates = "mean")
limits	numeric value, return only the specified number of rows (Default 1000)
perturbagen_time	numeric vector with perturbagen times (Default "all")

Value

data frame containing entity selected and the associated plate normalized log2 fold change

Examples

get_gcp_expression(cells = c("MCF7","PC3"))
get_gcp_expression(cells = c("MCF7","PC3"),filter_zscores=">2")
get_gcp_expression(perturbagens = "BRD-K31283835")
get_gcp_expression(histone_modification = "acetylation")

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