View source: R/permutationClustering.R
permutationClustering | R Documentation |
This function executes a ubuntu docker that produces a specific number of permutation to evaluate clustering.
permutationClustering(
group = c("sudo", "docker"),
scratch.folder,
file,
nPerm,
permAtTime,
percent,
range1 = 3,
range2 = 3,
separator,
logTen = 0,
clustering,
perplexity = 10,
seed = 1111,
rK = 0
)
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 file, with file name and extension included |
nPerm, |
number of permutations to perform the pValue to evaluate clustering |
permAtTime, |
number of permutations that can be computes in parallel |
percent, |
percentage of randomly selected cells removed in each permutation |
range1, |
first number of cluster for k means algorithm |
range2, |
last number of cluster for k means algorithm |
separator, |
separator used in count file, e.g. '\t', ',' |
logTen, |
1 if the count matrix is already in log10, 0 otherwise |
clustering, |
clustering method to use : "SIMLR" , "tSne", "griph" |
perplexity, |
Number of close neighbors for each point. This parameter is specific for tSne. Default value is 10.Setting this parameter when use a clustering method different by tSne will be ignored. |
seed, |
important value to reproduce the same results with same input |
rK, |
1 for rankGene algorithm 0 otherwise WARNING, very slow with this feature. This parameter is specific for SIMLR. Setting this parameter to 1 with other clustering methods will not give any different result to set the parameter to 0. |
VioPlot of silhouette cells value for each number of cluster used,clusterP file with clustering results for each permutation, killedCell file with removed cells in each permutation, clustering.output a sommarize file with general information for each cells.
Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
## Not run:
permutationClustering("docker","/home/lucastormreig/CASC2.0/permutationClustering/scratch/","/home/lucastormreig/CASC2.0/permutationClustering/Data/TOTAL.csv",4,2,10,3,4,separator=",",logTen=0,clustering="SIMLR",perplexity=0)
## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.