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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("readat")
AuthorRichard Cotton [cre, aut], Aditya Bhagwat [aut]
Bioconductor views DataImport GeneExpression OneChannel ProprietaryPlatforms Proteomics
Date of publicationNone
MaintainerRichard Cotton <richierocks@gmail.com>
LicenseGPL-3
Version1.2.0
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

Functions

aptamers Man page
as.ExpressionSet Man page
as.ExpressionSet.WideSomaLogicData Man page
as.matrix.WideSomaLogicData Man page
as.MSnSet Man page
as.MSnSet.WideSomaLogicData Man page
as.SummarizedExperiment Man page
as.SummarizedExperiment.WideSomaLogicData Man page
chromosomalPositions Man page
colnamesStartWithSeqId Man page
convertSeqIdToAptamer Man page
createSampleSubmission Man page
defunct Man page
ensemblIds Man page
extractSampleData Man page
getChecksum Man page
getChromosomalPositions Man page
getEnsemblIds Man page
getGoBiologicalProcesses Man page
getGoCellularComponents Man page
getGoMolecularFunctions Man page
getIntensities Man page
getIntensities.LongSomaLogicData Man page
getIntensities.WideSomaLogicData Man page
getKeggDefinitions Man page
getKeggModules Man page
getKeggPathways Man page
getMetadata Man page
getPfam Man page
getSampleData Man page
getSampleData.LongSomaLogicData Man page
getSampleData.WideSomaLogicData Man page
getSequenceData Man page
getSequencesWithLargestBetweenGroupVariation Man page
getUniProtKeywords Man page
goBiologicalProcess Man page
goCellularComponent Man page
goMolecularFunction Man page
isPass Man page
keggDefinitions Man page
keggDefinitions1129 Man page
keggModules Man page
keggModules1129 Man page
keggPathways Man page
keggPathways1129 Man page
melt.WideSomaLogicData Man page
pfam Man page
readAdat Man page
readat-defunct Man page
readComments Man page
readControls Man page
readFirstChar Man page
readSamples Man page
readSlides Man page
setChecksum Man page
setIntensities Man page
setMetadata Man page
setSampleData Man page
setSequenceData Man page
soma2eset Man page
uniprotKeywords Man page
WideSomaLogicData Man page
[.WideSomaLogicData Man page
WideSomaLogicDataAttributes Man page
writeSampleSubmissionForm Man page

Files

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

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