cometsc.Rd
This function executes a ubuntu docker for cometsc (https://github.com/MSingerLab/COMETSC)
cometsc( group = c("sudo", "docker"), file, scratch.folder, threads = 1, X = 0.15, K = 2, counts = c("True", "False"), skipvis = c("True", "False"), nCluster, separator )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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file, | a character string indicating the path of the file, with file name and extension included |
scratch.folder, | temporary folder where calculation is made |
threads, | integer refering to the max number of process run in parallel default 1 max the number of clusters under analysis, i.e. nCluster |
X, | from 0 to 1 argument for XL-mHG default 0.15, for more info see cometsc help. |
K, | the number of gene combinations to be considered., possible values 2, 3, 4, default 2. WARNING increasing the number of combinations makes the matrices very big |
counts, | if set to True it will graph the log(expression+1). To be used if unlogged data are provided |
skipvis, | set to True to skip visualizations |
nCluster, | number of interested cluster used for analysis |
separator, | separator used in count file, e.g. '\t', ',' |
folders with prefix output. More info in output at https://hgmd.readthedocs.io/en/latest/Output.html
Raffaele Calogero,raffaele.calogero [at] unito [dot] it, University of Torino
if (FALSE) { #running cometsc cometsc(group="docker", file="/Users/raffaelecalogero/Desktop/AXLN1/data/topx_veanno.csv", scratch.folder="/Users/raffaelecalogero/Desktop", threads=1, counts="True", skipvis="False", nCluster=8, separator=",") }