readat: Functionality to Read and Manipulate SomaLogic ADAT files

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

Author
Richard Cotton [cre, aut], Aditya Bhagwat [aut]
Date of publication
None
Maintainer
Richard Cotton <richierocks@gmail.com>
License
GPL-3
Version
1.0.0
URLs

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