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Oct 21, 2022
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Update mass spec classes #183

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7 changes: 3 additions & 4 deletions content/developers/how-to/commonMethodsAndClasses.md
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Expand Up @@ -15,14 +15,13 @@ searching in [BiocViews](/packages) for your data type.
+ FASTA -- [Biostrings][]`::readDNAStringSet()`
+ FASTQ -- [ShortRead][]`::readFastq()`
+ MS data (XML-based and mgf formats) -- [Spectra][]`::Spectra()`,
[MSnbase][]`::readMSData()`, [Spectra][]`::Spectra(source = MsBackendMgf::MsBackendMgf())`,
[MSnbase][]`::readMgfData()`
[Spectra][]`::Spectra(source = MsBackendMgf::MsBackendMgf())`

## Common Classes

+ Rectangular feature x sample data --
[SummarizedExperiment][]`::SummarizedExperiment()` (RNAseq count
matrix, microarray, ...)
matrix, microarray, quantitative proteomics, ...)
+ Genomic coordinates -- [GenomicRanges][]`::GRanges()` (1-based,
closed interval)
+ Genomic coordinates from multiple samples --
Expand All @@ -36,7 +35,7 @@ searching in [BiocViews](/packages) for your data type.
[MultiAssayExperiment][]`::MultiAssayExperiment()`
+ Single cell data --
[SingleCellExperiment][]`::SingleCellExperiment()`
+ Mass spec data -- [Spectra][]`::Spectra()`, [MSnbase][]`::MSnExp()`
+ Mass spec data -- [Spectra][]`::Spectra()`

[rtracklayer]: https://bioconductor.org/packages/rtracklayer
[Biostrings]: https://bioconductor.org/packages/Biostrings
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