readat: Functionality to Read and Manipulate SomaLogic ADAT files

This package contains functionality to import, transform and annotate data from ADAT files generated by the SomaLogic SOMAscan platform.

AuthorRichard Cotton [cre, aut], Aditya Bhagwat [aut]
Date of publicationNone
MaintainerRichard Cotton <richierocks@gmail.com>
LicenseGPL-3
Version1.0.0
https://bitbucket.org/graumannlabtools/readat

View on Bioconductor

Man pages

aptamers: Sequence data for the Somalogic SOMAscan assay

as.ExpressionSet: Convert objects into ExpressionSets or MSnSets.

as.SummarizedExperiment: Convert objects into SummarizedExperiments

chromosomalPositions: Chromosomal Positions by SomaLogic AptamerId

colnamesStartWithSeqId: Does the input contain Sequence ID column names?

convertSeqIdToAptamer: Convert SeqIds to Aptamers

createSampleSubmission: Create a SomaLogic Sample Submission Form

ensemblIds: Ensembl IDs by SomaLogic AptamerId

extractSampleData: Extract the sample datasets

getChromosomalPositions: Get Chromosomal Positions by AptamerId

getEnsemblIds: Get Ensembl IDs by AptamerId

getGoMolecularFunctions: GO definitions by AptamerId

getKeggDefinitions: KEGG definitions, modules, and pathways by AptamerId

getPfam: Get PFAM IDs by AptamerId

getSequencesWithLargestBetweenGroupVariation: Get sequences with the largest between group variation

getUniProtKeywords: Get UniProt Keywords by AptamerId

goMolecularFunction: GO definitions by SomaLogic AptamerId

isPass: Is the value a pass

keggDefinitions: KEGG definitions, modules, and pathways by SomaLogic...

melt.WideSomaLogicData: Melt a WideSomaLogicData object

pfam: PFAM IDs by SomaLogic AptamerId

readAdat: Read a SomaLogic data file

readat-defunct: Defunct objects in readat

readComments: Read SomaLogic Sample Submission Comments File

readControls: Read SomaLogic Sample Submission Controls File

readFirstChar: Read the first character of each line

readSamples: Read SomaLogic Sample Submission Samples File

readSlides: Read SomaLogic Sample Submission Slides File

sub-.WideSomaLogicData: Indexing for WideSomaLogicData objects

uniprotKeywords: UniProt Keywords by SomaLogic AptamerId

WideSomaLogicData: Create a WideSomaLogicData object

WideSomaLogicDataAttributes: Get WideSomaLogicData attributes

writeSampleSubmissionForm: Write a SomaLogic sample submission form

Files in this package

readat/DESCRIPTION
readat/NAMESPACE
readat/NEWS
readat/R
readat/R/SummarizedExperiment.R readat/R/checkIds.R readat/R/dataset-docs.R readat/R/defunct.R readat/R/extractSampleData.R readat/R/get-annotations.R readat/R/getSequencesWithLargestBetweenGroupVariation.R readat/R/list-utils.R readat/R/methods.R readat/R/read-sample-submision-input-files.R readat/R/readAdat.R readat/R/sfread.R readat/R/soma2eset.R readat/R/suppressSomeFeedback.R
readat/README.md
readat/build
readat/build/vignette.rds
readat/data
readat/data/aptamers.rda
readat/data/chromosomalPositions.rda
readat/data/ensembl.rda
readat/data/goBiologicalProcess.rda
readat/data/goCellularComponent.rda
readat/data/goMolecularFunction.rda
readat/data/keggDefinitions.rda
readat/data/keggModules.rda
readat/data/keggPathways.rda
readat/data/pfam.rda
readat/data/uniprotKeywords.rda
readat/inst
readat/inst/CITATION
readat/inst/doc
readat/inst/doc/introduction.R
readat/inst/doc/introduction.Rmd
readat/inst/doc/introduction.html
readat/inst/extdata
readat/inst/extdata/PLASMA.1.1k.20151030.adat.zip
readat/inst/extdata/PLASMA.1.3k.20151030.adat.zip
readat/inst/extdata/SOMAscan_1.3k_1.1k_dilutions.csv
readat/inst/extdata/comments.csv
readat/inst/extdata/controls.csv
readat/inst/extdata/samples.csv
readat/inst/extdata/slides.csv
readat/man
readat/man/WideSomaLogicData.Rd readat/man/WideSomaLogicDataAttributes.Rd readat/man/aptamers.Rd readat/man/as.ExpressionSet.Rd readat/man/as.SummarizedExperiment.Rd readat/man/chromosomalPositions.Rd readat/man/colnamesStartWithSeqId.Rd readat/man/convertSeqIdToAptamer.Rd readat/man/createSampleSubmission.Rd readat/man/ensemblIds.Rd readat/man/extractSampleData.Rd readat/man/getChromosomalPositions.Rd readat/man/getEnsemblIds.Rd readat/man/getGoMolecularFunctions.Rd readat/man/getKeggDefinitions.Rd readat/man/getPfam.Rd readat/man/getSequencesWithLargestBetweenGroupVariation.Rd readat/man/getUniProtKeywords.Rd readat/man/goMolecularFunction.Rd readat/man/isPass.Rd readat/man/keggDefinitions.Rd readat/man/melt.WideSomaLogicData.Rd readat/man/pfam.Rd readat/man/readAdat.Rd readat/man/readComments.Rd readat/man/readControls.Rd readat/man/readFirstChar.Rd readat/man/readSamples.Rd readat/man/readSlides.Rd readat/man/readat-defunct.Rd readat/man/sub-.WideSomaLogicData.Rd readat/man/uniprotKeywords.Rd readat/man/writeSampleSubmissionForm.Rd
readat/tests
readat/tests/testthat
readat/tests/testthat.R
readat/tests/testthat/hgnc_gene_symbols.rds
readat/tests/testthat/test-checkIds.R
readat/tests/testthat/test-methods.R
readat/tests/testthat/test-readAdat.R
readat/vignettes
readat/vignettes/introduction.Rmd

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