analyze: Call QUADrATiC with a query gene signature

In hiraethus/QuadraticAPI: A package to call Paul O'Reilly's QUADrATiC Connectivity Map software from R

Description

Call QUADrATiC with a query gene signature

Usage

analyze(query.gene.sig, analysis.set = "Drug_Name", num.rand.sigs = 2000,
  endpoint = getOption("quadratic.endpoint", default =
  "http://127.0.0.1:8090"))

Arguments

query.gene.sig	A data frame containing one column of probe IDs and a second with values of 1 where up-regulated and -1 where down-regulated.
analysis.set	Define how reference profiles are grouped into reference sets in QUADrATiC. Valid values are Drug_Name, Drug_Name+Cell_Line, Drug_Name+Cell_Line+Time, Drug_Name+Conc+Cell_Line and Drug_Name+Conc+Cell_Line+Time. Default is Drug_Name.
num.rand.sigs	The number of random signatures generated to estimate p-value. Default is 2000.
endpoint	The URL for QUADrATiC. Default is http://localhost:8090. This can also be set globally by setting the option 'quadratic.endpoint'.

Examples

estrogen.signature <- read.table('data/Estrogen.tsv', stringsAsFactors = F)
analyze(estrogen.signature)

hiraethus/QuadraticAPI documentation built on May 29, 2019, 1:18 p.m.