genesSelection: Genes selection from genesPrioritization output

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

Genes selection from genesPrioritization output

Description

This function executes a ubuntu docker that extracts the genes playin major role in clusterin from output of genesPrioritization

Usage

genesSelection(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nCluster,
  separator,
  seed = 111,
  sp = 0.8,
  clusterPermErr = 0.05,
  maxDeltaConfidence = 0.01,
  minLogMean = 0.05
)

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 file, with file name and extension included
nCluster	the number of clusters, where to run prioritization
separator	separator used in count file, e.g. '\t', ','
seed	important value to reproduce the same results with same input
sp	minimun number of percentage of cells that has to be in common in a cluster, between two permutations, default 0.8
clusterPermErr	probability error in depicting the number of clusters in each permutation, default = 0.05
maxDeltaConfidence	max value for Delta confidence for gene prioritization p-values.
minLogMean	min value for Log mean gene prioritization p-value. P-value indicates the importance of a gene in defining clusterization.

Value

....

Author(s)

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

Examples

## Not run: 
system("wget http://130.192.119.59/public/section4.1_examples.zip")
unzip("section4.1_examples.zip")
setwd("section4.1_examples")
genesSelection(group="docker",scratch.folder="/data/scratch/",file=paste(getwd(), "bmsnkn_5x100cells.txt", sep="/"), nCluster=5, separator="\t",  seed=111, sp=0.8, clusterPermErr=0.05, maxDeltaConfidence=0.01, minLogMean=0.05)

## End(Not run)

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