Common Bioconductor Methods and Classes

It is highly recommended to reuse existing methods for importing data as well as reuse already established classes and functionality rather than creating ‘new’ or repeating code. Here are some suggestions for importing different file types and commonly used Bioconductor classes. For more classes and functionality also try searching in BiocViews for your data type.

Importing

• GTF, GFF, BED, BigWig, …
  rtracklayer::import()
  
  
• FASTA
  Biostrings::readDNAStringSet()
  
  
• SAM / BAM
  Rsamtools::scanBam()
GenomicAlignments::readGAlignment*()
  
  
• VCF
  VariantAnnotation::readVcf()
  
  
• FASTQ
  ShortRead::readFastq()
  
  
• MS data (XML-based and mfg formats)
  MSnbase::readMSData()
MSnbase::readMgfData()

Common Classes

• DNA / RNA / AA sequences
  Biostrings::*Stringset()
  
  
• GeneSets
  GSEABase::GeneSet()
GSEABase::GeneSetCollection()
  
  
• 1-based, closed-interval genomic coordinates
  GenomicRanges::GRanges()
  
  
• rectangular freature x sample data (RNAseq count matrix, microarray, …)
  SummarizedExperiment::SummarizedExperiment()
  
  
• multi omics data
  MultiAssayExperiment::MultiAssayExperiment()
  
  
• single cell data
  SingleCellExperiment::SingleCellExperiment()
  
  
• mass spec data
  MSnbase::MSnExp()