A C D E F G H I L M N P R S T U V W
isobar-package | Analysis and quantitation of isobarically tagged MSMS proteomics data |
as.data.frame-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
as.data.frame-method | ProteinGroup objects |
as.data.frame.ProteinGroup | ProteinGroup objects |
calculate.dNSAF | dNSAF approximate abundance calculations. |
calculate.emPAI | emPAI approximate abundance calculations. |
class:IBSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
class:NoiseModel | NoiseModel objects |
class:ProteinGroup | ProteinGroup objects |
classLabels | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
classLabels-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
classLabels<- | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
classLabels<--method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
coerce-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
coerce-method | ProteinGroup objects |
combn.matrix | protein and peptide ratios |
combn.protein.tbl | protein and peptide ratios |
connect.nodes | Isobar reports |
correctIsotopeImpurities | IBSpectra preprocessing |
correctIsotopeImpurities-method | IBSpectra preprocessing |
create.meta.reports | Isobar reports |
create.reports | Isobar reports |
do.log | Log functions for IBSpectra objects |
do.log-method | Log functions for IBSpectra objects |
draw.boxplot | Isobar reports |
draw.protein.group | Isobar reports |
estimateRatio | IBSpectra analysis: Protein and peptide ratio calculation |
estimateRatio-method | IBSpectra analysis: Protein and peptide ratio calculation |
estimateRatioForPeptide | IBSpectra analysis: Protein and peptide ratio calculation |
estimateRatioForProtein | IBSpectra analysis: Protein and peptide ratio calculation |
estimateRatioNumeric | IBSpectra analysis: Protein and peptide ratio calculation |
estimateRatioNumeric-method | IBSpectra analysis: Protein and peptide ratio calculation |
exclude | IBSpectra preprocessing |
exclude-method | IBSpectra preprocessing |
ExponentialNoANoiseModel-class | NoiseModel objects |
ExponentialNoiseModel-class | NoiseModel objects |
fitCauchy | Fit weighted and unweighted Cauchy and Normal distributions |
fitGaussianMixture | Fit weighted and unweighted Cauchy and Normal distributions |
fitGumbel | Fit weighted and unweighted Cauchy and Normal distributions |
fitNorm | Fit weighted and unweighted Cauchy and Normal distributions |
fitNormalCauchyMixture | Fit weighted and unweighted Cauchy and Normal distributions |
fitTd | Fit weighted and unweighted Cauchy and Normal distributions |
fitWeightedNorm | Fit weighted and unweighted Cauchy and Normal distributions |
get.log | Log functions for IBSpectra objects |
get.log-method | Log functions for IBSpectra objects |
get.pep.group | ProteinGroup objects |
getMultUnifDensity | IBSpectra analysis: Protein and peptide ratio calculation |
getMultUnifPValues | IBSpectra analysis: Protein and peptide ratio calculation |
getProteinInfoFromBioDb | Methods for Function proteinInfo |
getProteinInfoFromBiomart | Methods for Function proteinInfo |
getProteinInfoFromNextProt | Methods for Function proteinInfo |
getProteinInfoFromUniprot | Methods for Function proteinInfo |
group-specific | Peptide specificities |
groupMemberPeptides | Peptide info for protein group members |
GROUPSPECIFIC | Peptide specificities |
human.protein.names | Info on proteins |
IBSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
IBSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
IBSpectraTypes | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
ibspiked_set1 | Isobar Data packages |
ibspiked_set2 | Isobar Data packages |
indistinguishableProteins | ProteinGroup objects |
indistinguishableProteins-method | ProteinGroup objects |
initialize-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
initialize-method | NoiseModel objects |
initialize.env | Isobar reports |
InverseNoANoiseModel-class | NoiseModel objects |
InverseNoiseModel-class | NoiseModel objects |
is.logged | Log functions for IBSpectra objects |
is.logged-method | Log functions for IBSpectra objects |
isobar | Analysis and quantitation of isobarically tagged MSMS proteomics data |
isobar-analysis | IBSpectra analysis: Protein and peptide ratio calculation |
isobar-import | Loading data into IBSpectra objects using readIBSpectra |
isobar-plots | IBSpectra plots |
isobar-preprocessing | IBSpectra preprocessing |
isobar-reports | Isobar reports |
isotopeImpurities | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
isotopeImpurities-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
isotopeImpurities<- | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
isotopeImpurities<--method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
iTRAQ4plexSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
iTRAQ4plexSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
iTRAQ8plexSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
iTRAQ8plexSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
iTRAQSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
iTRAQSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
load.properties | Isobar reports |
lowIntensity | NoiseModel objects |
lowIntensity-method | NoiseModel objects |
lowIntensity<- | NoiseModel objects |
lowIntensity<--method | NoiseModel objects |
maplot | IBSpectra plots |
maplot-method | IBSpectra plots |
maplot.protein | Ratio intensity plot for individual proteins |
maplot2 | IBSpectra plots |
maplot2-method | IBSpectra plots |
modifs | Isobar reports |
my.protein.info | Info on proteins |
n.observable.peptides | emPAI approximate abundance calculations. |
naRegion | NoiseModel objects |
naRegion-method | NoiseModel objects |
naRegion<- | NoiseModel objects |
naRegion<--method | NoiseModel objects |
noise.model.hcd | Isobar Data packages |
noiseFunction | NoiseModel objects |
noiseFunction-method | NoiseModel objects |
NoiseModel | NoiseModel objects |
NoiseModel-class | NoiseModel objects |
NoiseModel-method | NoiseModel objects |
normalize | IBSpectra preprocessing |
number.ranges | Helper function to transform number lists to ranges |
parameter | NoiseModel objects |
parameter-method | NoiseModel objects |
parameter<- | NoiseModel objects |
parameter<--method | NoiseModel objects |
paste0 | Isobar util functions |
peptide.count | Peptide counts, spectral counts and sequence coverage for ProteinGroup objects. |
peptideNProtein | ProteinGroup objects |
peptideNProtein-method | ProteinGroup objects |
peptideRatios | protein and peptide ratios |
peptides | ProteinGroup objects |
peptides-method | ProteinGroup objects |
peptideSpecificity | ProteinGroup objects |
peptideSpecificity-method | ProteinGroup objects |
plotRatio | IBSpectra plots |
plotRatio-method | IBSpectra plots |
print_longtablehdr | Isobar reports |
print_longtablehdr_peptide | Isobar reports |
protein.ac | ProteinGroup objects |
protein.ac-method | ProteinGroup objects |
protein.g | ProteinGroup objects |
protein.g-method | ProteinGroup objects |
ProteinGroup | ProteinGroup objects |
proteinGroup | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
ProteinGroup-class | ProteinGroup objects |
ProteinGroup-method | ProteinGroup objects |
proteinGroup-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
proteinGroup<- | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
proteinGroup<--method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
proteinGroupTable | ProteinGroup objects |
proteinGroupTable-method | ProteinGroup objects |
proteinInfo | Methods for Function proteinInfo |
proteinInfo-method | Methods for Function proteinInfo |
proteinInfo-methods | Methods for Function proteinInfo |
proteinInfo<- | Methods for Function proteinInfo |
proteinInfo<--method | Methods for Function proteinInfo |
proteinInfoIsOnSpliceVariants | Methods for Function proteinInfo |
proteinRatios | protein and peptide ratios |
protGgdata | IBSpectra plots |
protGgdata-method | IBSpectra plots |
raplot | IBSpectra plots |
raplot-method | IBSpectra plots |
ratiosReshapeWide | Reshape output of proteinRatios into wide format |
read.mzid | Loading data into IBSpectra objects using readIBSpectra |
readIBSpectra | Loading data into IBSpectra objects using readIBSpectra |
readIBSpectra-method | Loading data into IBSpectra objects using readIBSpectra |
readProteinGroup | ProteinGroup objects |
reporter-specific | Peptide specificities |
reporterData | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterData-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterData<- | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterData<--method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterIntensities | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterIntensities-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterIntensities<- | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterIntensities<--method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterIntensityPlot | IBSpectra plots |
reporterIntensityPlot-method | IBSpectra plots |
reporterIntensityPlot-methods | IBSpectra plots |
reporterMasses | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterMasses-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterMasses<- | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterMasses<--method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterMassPrecision | IBSpectra plots |
reporterMassPrecision-method | IBSpectra plots |
reporterProteins | ProteinGroup objects |
reporterProteins-method | ProteinGroup objects |
REPORTERSPECIFIC | Peptide specificities |
reporterTagMasses | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterTagMasses-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterTagNames | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
reporterTagNames-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
sanitize | Helper function for LaTeX export |
sequence.coverage | Peptide counts, spectral counts and sequence coverage for ProteinGroup objects. |
shared.ratios | Shared ratio calculation |
shared.ratios.sign | Plot and get significantly shared ratios. |
show-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
show-method | NoiseModel objects |
show-method | ProteinGroup objects |
SPECIFICITIES | Peptide specificities |
specificities | Peptide specificities |
spectra.count | Peptide counts, spectral counts and sequence coverage for ProteinGroup objects. |
spectrumSel | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
spectrumSel-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
spectrumTitles | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
spectrumTitles-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
spectrumToPeptide | ProteinGroup objects |
spectrumToPeptide-method | ProteinGroup objects |
stddev | NoiseModel objects |
stddev-method | NoiseModel objects |
subsetIBSpectra | Subset IBSpectra objects |
subtractAdditiveNoise | IBSpectra preprocessing |
subtractAdditiveNoise-method | IBSpectra preprocessing |
summarize.ratios | protein and peptide ratios |
summary.ProteinGroup | ProteinGroup objects |
tikz.proteingroup | Isobar reports |
TMT2plexSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
TMT2plexSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
TMT6plexSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
TMT6plexSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
TMTSpectra | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
TMTSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
transform_pepmodif | Isobar reports |
UNSPECIFIC | Peptide specificities |
unspecific | Peptide specificities |
variance | NoiseModel objects |
variance-method | NoiseModel objects |
VARMETADATA | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
weightedMean | protein and peptide ratios |
weightedMean-method | protein and peptide ratios |
weightedVariance | protein and peptide ratios |
weightedVariance-method | protein and peptide ratios |
write.xls.report | Isobar reports |
writeData | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
writeData-method | IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data |
writeIBSpectra | Write IBSpectra file as CSV in a format readable by readIBSpectra. |