runCamera: A wrapper over CAMERA test.

In vivekbhr/vivlib: An R package for useful bioinformatics wrappers

Description

A wrapper over CAMERA test.

Usage

runCamera(fcountOutput, design, bmGeneNames,
  moduleFile = "msigdb.v5.0.symbols.gmt", outfileName)

Arguments

fcountOutput	A tab-seperated file containing gene names followed by fcountOutput
design	A tab-seperated file containing design information (colnames, condition). colnames should correspond to columns in count file and condition could be control/test or any set of factors.
bmGeneNames	Optionally provide alternative gene symbols downloaded from biomart as a tab-seperated file. The columns should be ("ensembl_gene_id","external_gene_id")
moduleFile	A file with modules to test. Download from http://software.broadinstitute.org/gsea/msigdb/index.jsp
outfileName	Output pdf file name.

Value

CAMERA result object.

Examples

## Not run: 
fc <- system.file("extdata", "fcount_mouse.tsv", package="vivlib")
design <- data.frame(row.names = c(paste0("cnt_", 1:3), paste0("KD_",1:3)),
                     condition = rep(c("cnt","KD"), each = 3) )

runCamera(fcountOutput,design,bmGeneNames,name="myVoomInput",outfileName = "test")

## End(Not run)

vivekbhr/vivlib documentation built on May 3, 2019, 6:13 p.m.