Calculation of physicochemical amino acid properties for APEX
Calculation of physicochemical amino acid properties for APEX.
## Default S3 method: apexFeatures(x, ...) ## S3 method for class 'apexFeatures' print(x, ...)
x |
a mandatory data frame containing the variables in the model.
The data frame requires the columns |
... |
future extensions. |
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.
An object of class apexFeatures.
George Rosenberger gr2578@cumc.columbia.edu
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).
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)
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