cellSigAnalysis: Hits function analysis

In OperaMate: An R package of Data Importing, Processing and Analysis for Opera High Content Screening System

Description

Performs function analysis using gProfileR

Usage

cellSigAnalysis(object, genemap, organism, type = c("High", "Low"),
  file = NULL, ...)

Arguments

object	a cellData object
genemap	a data frame, the well-gene specification table
organism	organism name.
type	include both high and low expressed hits or one of them.
file	the filename of the enrichment table (default: disabled)
...	the arguments of gprofiler.

Details

genemap must include colnames "Barcode","Well","GeneSymbol". organism name can be referred to g:Profiler tool. For example, human: hsapiens, mouse: mmusculus.

Value

a data frame of the functional report from gProfiler

Examples

data(demoCell)
genemap <- read.csv(file.path(system.file("Test", package = "OperaMate"),
"demoData", "genemap.csv"), stringsAsFactors = FALSE)
chart <- cellSigAnalysis(oneCell, genemap, organism = "mmusculus")
head(chart)

Example output

Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to biit.cs.ut.ee port 80: Connection refused
Warning message:
In cellSigAnalysis(oneCell, genemap, organism = "mmusculus") :
  Function gProfile failed.
NULL

OperaMate documentation built on Nov. 17, 2017, 1:55 p.m.