dimsum: Run DiMSum pipeline

Description Usage Arguments Value

View source: R/dimsum.R

Description

This function runs the DiMSum pipeline.

Usage

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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,
  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,
  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)

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)

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)

Value

Nothing


lehner-lab/DiMSum documentation built on Sept. 15, 2021, 12:43 a.m.