geneVisualization2: GeneVisualization2

View source: R/geneVisualization2.R

geneVisualization2R Documentation

GeneVisualization2

Description

This function executes a ubuntu docker that performs geneVisualization

Usage

geneVisualization2(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  clustering.output,
  geneList,
  separator,
  finalName,
  pvalueFile,
  threshold
)

Arguments

group

a character string. Two options: sudo or docker, depending to which group the user belongs

scratch.folder

a character string indicating the path of the scratch folder

file

a character string indicating the path of the count matrix

clustering.output

a character string indicating the path of the clustering.output matrix

geneList

a character string indicating the path of the geneList matrix (no header, no row names)

separator

separator used in count file, e.g. '\t', ','

finalName

name used for plot.

pvalueFile

name for pvalue file.

threshold

threshold value.

Value

plot

Author(s)

Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

Examples

## Not run: 
dir.create("scratch")
geneVisualization2(group="docker", scratch.folder="/scratch", file="/example/log2cpm.csv",clustering.output="/example/log2cpm_fake_clustering.output.csv",geneList="/example/geneList2.csv",separator=",",finalName="yo",pvalueFile="/example/log2cpmfisher.csv",threshold=0.05)

## End(Not run)

kendomaniac/rCASC documentation built on July 3, 2024, 6:05 a.m.