geneVisualization2: GeneVisualization2

In kendomaniac/CASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

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/CASC documentation built on Oct. 4, 2023, 11:10 a.m.