R: Estimating Absolute Protein Quantities from Label-Free LC-MS/MS Proteomics Data

# Estimating Absolute Protein Quantities from Label-Free LC-MS/MS Proteomics Data

## Documentation for package ‘aLFQ’ version 1.3.6

- DESCRIPTION file

## Help Pages

aLFQ-package | aLFQ
AbsoluteQuantification | Absolute label-free quantification of mass spectrometry proteomics experiments
AbsoluteQuantification.default | Absolute label-free quantification of mass spectrometry proteomics experiments
ALF | Generate ALF report
ALF.default | Generate ALF report
aLFQ | aLFQ
APEX | Training, testing and validation of APEX peptide observability models
APEX.default | Training, testing and validation of APEX peptide observability models
apexFeatures | Calculation of physicochemical amino acid properties for APEX
apexFeatures.default | Calculation of physicochemical amino acid properties for APEX
APEXMS | Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
APEX_LCQ | Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
APEX_ORBI | Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
cval | Absolute label-free quantification of mass spectrometry proteomics experiments
cval.AbsoluteQuantification | Absolute label-free quantification of mass spectrometry proteomics experiments
cval.APEX | Training, testing and validation of APEX peptide observability models
cval.default | Absolute label-free quantification of mass spectrometry proteomics experiments
export | Absolute label-free quantification of mass spectrometry proteomics experiments
export.AbsoluteQuantification | Absolute label-free quantification of mass spectrometry proteomics experiments
export.default | Absolute label-free quantification of mass spectrometry proteomics experiments
hist.AbsoluteQuantification | Absolute label-free quantification of mass spectrometry proteomics experiments
import | import of mass spectrometry proteomics data analysis software reports.
import.default | import of mass spectrometry proteomics data analysis software reports.
LUDWIGMS | Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry..
LUDWIG_SRM | Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry..
PeptideInference | Peptide inference for aLFQ import data frame
PeptideInference.default | Peptide inference for aLFQ import data frame
pivot | Absolute label-free quantification of mass spectrometry proteomics experiments
pivot.AbsoluteQuantification | Absolute label-free quantification of mass spectrometry proteomics experiments
pivot.default | Absolute label-free quantification of mass spectrometry proteomics experiments
plot.AbsoluteQuantification | Absolute label-free quantification of mass spectrometry proteomics experiments
plot.APEX | Training, testing and validation of APEX peptide observability models
predict.AbsoluteQuantification | Absolute label-free quantification of mass spectrometry proteomics experiments
predict.APEX | Training, testing and validation of APEX peptide observability models
print.AbsoluteQuantification | Absolute label-free quantification of mass spectrometry proteomics experiments
print.APEX | Training, testing and validation of APEX peptide observability models
print.apexFeatures | Calculation of physicochemical amino acid properties for APEX
ProteinInference | Protein inference for aLFQ import data frame
ProteinInference.default | Protein inference for aLFQ import data frame
proteotypic | Prediction of the flyability of proteotypic peptides
proteotypic.default | Prediction of the flyability of proteotypic peptides
UPS2 | Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
UPS2MS | Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
UPS2_LFQ | Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
UPS2_SC | Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
UPS2_SRM | Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.