dimsum: Run DiMSum pipeline
In lehner-lab/DiMSum: A pipeline for processing deep mutational scanning data

dimsum

R Documentation

Run DiMSum pipeline

Description

This function runs the DiMSum pipeline.

Usage

dimsum(
  runDemo = F,
  fastqFileDir = NULL,
  fastqFileExtension = ".fastq",
  gzipped = T,
  stranded = T,
  paired = T,
  barcodeDesignPath = NULL,
  barcodeErrorRate = 0.25,
  experimentDesignPath = NULL,
  experimentDesignPairDuplicates = F,
  barcodeIdentityPath = NULL,
  countPath = NULL,
  synonymSequencePath = NULL,
  cutadaptCut5First = NULL,
  cutadaptCut5Second = NULL,
  cutadaptCut3First = NULL,
  cutadaptCut3Second = NULL,
  cutadapt5First = NULL,
  cutadapt5Second = NULL,
  cutadapt3First = NULL,
  cutadapt3Second = NULL,
  cutadaptMinLength = 50,
  cutadaptErrorRate = 0.2,
  cutadaptOverlap = 3,
  vsearchMinQual = 30,
  vsearchMaxQual = 41,
  vsearchMaxee = 0.5,
  vsearchMinovlen = 10,
  outputPath = "./",
  projectName = "DiMSum_Project",
  wildtypeSequence = NULL,
  permittedSequences = NULL,
  reverseComplement = F,
  sequenceType = "auto",
  mutagenesisType = "random",
  transLibrary = F,
  transLibraryReverseComplement = F,
  bayesianDoubleFitness = F,
  bayesianDoubleFitnessLamD = 0.025,
  fitnessMinInputCountAll = "0",
  fitnessMinInputCountAny = "0",
  fitnessMinOutputCountAll = "0",
  fitnessMinOutputCountAny = "0",
  fitnessHighConfidenceCount = 10,
  fitnessDoubleHighConfidenceCount = 50,
  fitnessNormalise = T,
  fitnessErrorModel = T,
  indels = "none",
  maxSubstitutions = 2,
  mixedSubstitutions = F,
  retainIntermediateFiles = F,
  splitChunkSize = 3758096384,
  retainedReplicates = "all",
  startStage = 0,
  stopStage = 5,
  numCores = 1
)

Arguments

`runDemo`	Run the DiMSum demo (default:F)
`fastqFileDir`	Path to directory containing input FASTQ files (required for WRAP)
`fastqFileExtension`	FASTQ file extension (default:'.fastq')
`gzipped`	Are FASTQ files are gzipped? (default:T)
`stranded`	Is the library design stranded? (default:T)
`paired`	Is the library design paired-end? (default:T)
`barcodeDesignPath`	Path to barcode design file (tab-separated plain text file with barcode design)
`barcodeErrorRate`	Maximum allowed error rate for barcode to be matched (default:0.25)
`experimentDesignPath`	Path to Experimental Design File (required if '–runDemo'=F)
`experimentDesignPairDuplicates`	Are multiple instances of FASTQ files in the Experimental Design File permitted? (default:F)
`barcodeIdentityPath`	Path to Variant Identity File (tab-separated plain text file mapping barcodes to variants)
`countPath`	Path to Variant Count File for analysis with STEAM only (tab-separated plain text file with sample counts for all variants)
`synonymSequencePath`	Path to Synonym Sequences File with coding sequences for which synonymous variant fitness should be quantified (default: plain text file with one coding nucleotide sequence per line)
`cutadaptCut5First`	Remove fixed number of bases from start (5') of first (or only) read before constant region trimming (optional)
`cutadaptCut5Second`	Remove fixed number of bases from start (5') of second read in pair before constant region trimming (optional)
`cutadaptCut3First`	Remove fixed number of bases from end (3') of first (or only) read before constant region trimming (optional)
`cutadaptCut3Second`	Remove fixed number of bases from end (3') of second read in pair before constant region trimming (optional)
`cutadapt5First`	Sequence of 5' constant region to be trimmed from first (or only) read (optional)
`cutadapt5Second`	Sequence of 5' constant region to be trimmed from second read in pair (optional)
`cutadapt3First`	Sequence of 3' constant region to be trimmed from first (or only) read (default: reverse complement of '–cutadapt5Second')
`cutadapt3Second`	Sequence of 3' constant region to be trimmed from second read in pair (default: reverse complement of '–cutadapt5First')
`cutadaptMinLength`	Discard reads shorter than LENGTH after trimming (default:50)
`cutadaptErrorRate`	Maximum allowed error rate for trimming constant regions (default:0.2)
`cutadaptOverlap`	Minimum overlap between read and constant region for trimming (default:3)
`vsearchMinQual`	Minimum Phred base quality score required to retain read or read pair (default:30)
`vsearchMaxQual`	Maximum Phred base quality score accepted when reading (and used when writing) FASTQ files; cannot be greater than 93 (default:41)
`vsearchMaxee`	Maximum number of expected errors tolerated to retain read or read pair (default:0.5)
`vsearchMinovlen`	Discard read pair if the alignment length is shorter than this (default:10)
`outputPath`	Path to directory to use for output files (default:'./' i.e. current working directory)
`projectName`	Project name and directory where results are to be saved (default:'DiMSum_Project')
`wildtypeSequence`	Wild-type nucleotide sequence (A/C/G/T). Lower-case bases (a/c/g/t) indicate internal constant regions to be removed (required if '–runDemo'=F)
`permittedSequences`	Nucleotide sequence of IUPAC ambiguity codes (A/C/G/T/R/Y/S/W/K/M/B/D/H/V/N) with length matching the number of mutated positions (i.e upper-case letters) in '–wildtypeSequence' (default:N i.e. any substitution mutation allowed)
`reverseComplement`	Reverse complement sequence (default:F)
`sequenceType`	Coding potential of sequence: either 'noncoding', 'coding' or 'auto'. If the specified wild-type nucleotide sequence ('–wildtypeSequence') has a valid translation without a premature STOP codon, it is assumed to be 'coding' (default:'auto')
`mutagenesisType`	Whether mutagenesis was performed at the nucleotide or codon/amino acid level; either 'random' or 'codon' (default:'random')
`transLibrary`	Paired-end reads correspond to distinct molecules? (default:F)
`transLibraryReverseComplement`	Reverse complement second read in pair (default:F)
`bayesianDoubleFitness`	In development: improve double mutant fitness estimates using Bayesian framework (DISABLED: still in development)
`bayesianDoubleFitnessLamD`	In development: Poisson distribution for score likelihood (default:0.025)
`fitnessMinInputCountAll`	Minimum input read count (in all replicates) to be retained during fitness calculations (default:0)
`fitnessMinInputCountAny`	Minimum input read count (in any replicate) to be retained during fitness calculations (default:0)
`fitnessMinOutputCountAll`	Minimum output read count (in all replicates) to be retained during fitness calculations (default:0)
`fitnessMinOutputCountAny`	Minimum output read count (in any replicates) to be retained during fitness calculations (default:0)
`fitnessHighConfidenceCount`	In development: minimum mean input read count for high confidence variants (default:10)
`fitnessDoubleHighConfidenceCount`	In development: minimum input replicate read count for doubles used to derive prior for Bayesian doubles correction (default:50)
`fitnessNormalise`	Normalise fitness values to minimise inter-replicate differences (default:T)
`fitnessErrorModel`	Fit fitness error model (default:T)
`indels`	Indel variants to be retained: either 'all', 'none' or a comma-separated list of sequence lengths (default:'none')
`maxSubstitutions`	Maximum number of nucleotide or amino acid substitutions for coding or non-coding sequences respectively (default:2)
`mixedSubstitutions`	For coding sequences, are nonsynonymous variants with silent/synonymous substitutions in other codons allowed? (default:F)
`retainIntermediateFiles`	Should intermediate files be retained? Intermediate files can be many gigabytes, but are required to rerun DiMSum starting at intermediate pipeline stages (default:F)
`splitChunkSize`	Internal: FASTQ file split chunk size in bytes (default:3758096384)
`retainedReplicates`	Comma-separated list of (integer) experiment replicates to retain or 'all' (default:'all')
`startStage`	(Re-)Start DiMSum at a specific pipeline stage (default:0)
`stopStage`	Stop DiMSum at a specific pipeline stage (default:5)
`numCores`	Number of available CPU cores. All pipeline stages make use of parallel computing to decrease runtime if multiple cores are available (default:1)