GeneVisualization2

This function executes a ubuntu docker that performs geneVisualization

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

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

Examples

if (FALSE) {
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)
}