apexFeatures: Calculation of physicochemical amino acid properties for APEX

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

Description

Calculation of physicochemical amino acid properties for APEX.

Usage

## Default S3 method:
apexFeatures(x, ...)
## S3 method for class 'apexFeatures'
print(x, ...)

Arguments

x	a mandatory data frame containing the variables in the model. The data frame requires the columns "peptide_sequence", "apex". The data may contain training data (with boolean "apex" and test data (with "apex"=NA))
...	future extensions.

Details

The apexFeatures function computes the APEX or PeptideSieve features (Mallick et al., 2006; Vogel et al., 2008) based on AAindex (Kawashima et al., 2008) and returns them in an apexFeatures object for further usage in the APEX module.

Value

An object of class apexFeatures.

Author(s)

George Rosenberger [e-mail]

References

Kawashima, S. et al. AAindex: amino acid index database, progress report 2008. Nucleic Acids Research 36, D202-5 (2008).

Mallick, P. et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotech 25, 125-131 (2006).

Vogel, C. & Marcotte, E. M. Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data. Nat Protoc 3, 1444-1451 (2008).

See Also

import, ProteinInference, AbsoluteQuantification, ALF, APEX, proteotypic

Examples

data(APEXMS)

# APEX_ORBI
APEX_ORBI<-head(APEX_ORBI,20) # Remove this line for real applications
APEX_ORBI.af <- apexFeatures(APEX_ORBI)
print(APEX_ORBI.af)

# APEX_LCQ
APEX_LCQ<-head(APEX_LCQ,20) # Remove this line for real applications
APEX_LCQ.af <- apexFeatures(APEX_LCQ)
print(APEX_LCQ.af)

aLFQ documentation built on Jan. 8, 2020, 5:09 p.m.