gibbsR: gibbsR

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

gibbsR

Description

This function creates performs motif search in peptides. It was developed to use gibbscluster on TCR CDR3 peptide sequences

Usage

gibbsR(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  resFolderCustom = "NULL",
  jobName,
  nCluster,
  motifLength,
  maxDelLength,
  maxInsLength,
  numbOfSeed,
  penalityFactorIntCluster = 0.8,
  backGroundAminoFreq = 2,
  seqWeightType = 1
)

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	path to peptide file,
resFolderCustom	optional parameter. Default will store the results in fastqPath otherwise will store the results in resFolderCustom path.
jobName	identify of the sample
nCluster	number of clusters to be generated
motifLength	length of the motif to be searched
maxDelLength	max length of deletions in the peptide search, expressed in number of aa
maxInsLength	max length of insertion in the peptide search, expressed in number of aa
numbOfSeed	number of initial configurations to be used to detect the highest KLD sum
penalityFactorIntCluster	default 0.8,
backGroundAminoFreq	two value 1 defined by uniprot and 2 defined by the dataset under analysis
seqWeightType	sequence weighting type: default 1, faster but less precise, 2 slower but more precise, 3 none

Value

an indexed genome compliant with 10XGenomics cellranger

Author(s)

Luca Alessandrì

Examples

## Not run: 
library(rCASC)
dir.create("scratch")
scratch.folder=paste(getwd(),"scratch",sep="/")
fastqPath=paste(getwd(),"fastq",sep="/")
resFolder=paste(getwd(),"resFolder",sep="/")
dir.create(resFolder)

gibbsR(group="docker",scratch.folder=scratch.folder,file=file,resFolderCustom=results,jobName="test",nCluster=8,motifLength=4,maxDelLength=4,maxInsLength=4,numbOfSeed=4,penalityFactorIntCluster=0.8,backGroundAminoFreq=2,seqWeightType=1) 

newFolder=paste(results,"res",list.files(paste(results,"res",sep="/")),"cores",sep="/")

## End(Not run)

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