From 13de4e630027c7788c12e5a145b86181bffb9143 Mon Sep 17 00:00:00 2001 From: Laurent Gatto Date: Thu, 20 Oct 2022 22:52:30 +0200 Subject: [PATCH] Update mass spec classes Removing MSnbase, replaced by Spectra, which is now recommended. Note, that this page seemed outdated on the Bioc website. --- content/developers/how-to/commonMethodsAndClasses.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/content/developers/how-to/commonMethodsAndClasses.md b/content/developers/how-to/commonMethodsAndClasses.md index c8fa4e93c..6d4500883 100644 --- a/content/developers/how-to/commonMethodsAndClasses.md +++ b/content/developers/how-to/commonMethodsAndClasses.md @@ -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 -- @@ -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