get_L1000ph1_expression: Retrieve Broad L1000 data from LINCS Phase 1, weighted...

Description Usage Arguments Value Examples

View source: R/get_L1000ph1_expression.R

Description

Retrieve Broad L1000 data from LINCS Phase 1, weighted average of replicates z-scores

Usage

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get_L1000ph1_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

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get_L1000ph1_expression(genes = c("EGF","RHEB"))
get_L1000ph1_expression(cells = c("MCF7","PC3"),filter_zscores=">2")
get_L1000ph1_expression(cells = c("MCF7","PC3"),filter_zscores=">2")
get_L1000ph1_expression(perturbagens = c("BRD-K55966568","BRD-K97056771"))

schurerlab/LINCSanalytics documentation built on Jan. 30, 2018, 1:15 a.m.