Package cleaver. December 13, 2018
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1 Version Date Title Cleavage of Polypeptide Sequences Package cleaver December 13, 2018 Maintainer Sebastian Gibb Depends R (>= 3.0.0), methods, Biostrings (>= ) Imports S4Vectors, IRanges Suggests testthat (>= 0.8), knitr, BiocStyle (>= ), BRAIN, UniProt.ws (>= 2.1.4) Description In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: License GPL (>= 3) URL BugReports LazyLoad yes VignetteBuilder knitr biocviews Proteomics git_url git_branch RELEASE_3_8 git_last_commit e9242ec git_last_commit_date Date/Publication Author Sebastian Gibb [aut, cre] R topics documented: cleaver-package cleave Index 9 1
2 2 cleave cleaver-package Cleavage of polypeptide sequences Description Details This package cleaves polypeptide sequences. It provides three functions: cleave, cleavageranges and cleavagesites. The cleavage rules are taken from: enzymes.html Package: cleaver License: GPL (>= 3) URL: Author(s) Sebastian Gibb References Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A.; "Protein Identification and Analysis Tools on the ExPASy Server". (In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005). See Also cleave, cleavageranges and cleavagesites. cleave Cleavage of polypeptide sequences Description Usage This functions cleave polypeptide sequences. Use cleavagesites to find the cleavage sites, cleavageranges to find the cleavage ranges and cleave to get the cleavage products. ## S4 method for signature 'character' cleave(x, enzym = "trypsin", missedcleavages = 0, custom = NULL, unique = TRUE) ## S4 method for signature 'AAString'
3 cleave 3 cleave(x, enzym = "trypsin", missedcleavages = 0, custom = NULL, unique = TRUE) ## S4 method for signature 'AAStringSet' cleave(x, enzym = "trypsin", missedcleavages = 0, custom = NULL, unique = TRUE) ## S4 method for signature 'character' cleavageranges(x, enzym = "trypsin", missedcleavages = 0, custom = NULL) ## S4 method for signature 'AAString' cleavageranges(x, enzym = "trypsin", missedcleavages = 0, custom = NULL) ## S4 method for signature 'AAStringSet' cleavageranges(x, enzym = "trypsin", missedcleavages = 0, custom = NULL) ## S4 method for signature 'character' cleavagesites(x, enzym = "trypsin", custom = NULL) ## S4 method for signature 'AAString' cleavagesites(x, enzym = "trypsin", custom = NULL) ## S4 method for signature 'AAStringSet' cleavagesites(x, enzym = "trypsin", custom = NULL) Arguments x Details polypeptide sequences. enzym character, cleavage rule. missedcleavages numeric, number of missed cleavages. custom unique character, of length 1 or 2. Could be used to define own cleaveage rules. The first element would be the pattern and the optional second element would be an exception (non-cleavage) pattern. Perl-like regular expressions are supported, see gregexpr for details. If custom is set the enzym is ignored. logical, if TRUE all duplicated cleavage products per peptide are removed. The cleavage rules are taken from: enzymes.html Cleavage rules (cleavage between P1 and P1 ): Rule name P4 P3 P2 P1 P1 arg-c proteinase R - asp-n endopeptidase D bnps-skatole-c W - caspase1 F,W,Y,L - H,A,T D not P,E,D,Q, caspase2 D V A D not P,E,D,Q,
4 4 cleave caspase3 D M Q D not P,E,D,Q, caspase4 L E V D not P,E,D,Q, caspase5 L,W E H D - caspase6 V E H,I D not P,E,D,Q, caspase7 D E V D not P,E,D,Q, caspase8 I,L E T D not P,E,D,Q, caspase9 L E H D - caspase10 I E A D - chymotrypsin-high F,Y not P W not M,P chymotrypsin-low F,L,Y not P W not M,P M not P,Y H not D,M,P,W clostripain R - cnbr M - enterokinase D,E D,E D,E K - factor xa A,F,G,I,L,T,V,M D,E G R - formic acid D - glutamyl endopeptidase D - granzyme-b I E P D - hydroxylamine N G iodosobenzoic acid W - lysc K - lysn K neutrophil elastase A,V - ntcb C pepsin1.3 - not H,K,R not P not R F,L,W,Y - not H,K,R not P F,L,W,Y - pepsin - not H,K,R not P not R F,L - not H,K,R not P F,L - proline endopeptidase - - not H,K,R P not P proteinase k A,E,F,I,L,T,V,W,Y - staphylococcal peptidase i - - not E E - thermolysin not D,E A,F,I,L,M,V thrombin - - G R G A,F,G,I,L,T,V,M A,F,G,I,L,T,V,W P R not D,E trypsin K,R not P - - W K P - - M R P Exceptions: Rule name Enzyme name P4 P3 P2 P1 P1 P2 trypsin - - C,D K D C K H,Y C R K R R H,R - Rule name Enzyme name
5 cleave 5 arg-c proteinase Arg-C proteinase asp-n endopeptidase Asp-N endopeptidase bnps-skatole-c BNPS-Skatole caspase1 Caspase 1 caspase2 Caspase 2 caspase3 Caspase 3 caspase4 Caspase 4 caspase5 Caspase 5 caspase6 Caspase 6 caspase7 Caspase 7 caspase8 Caspase 8 caspase9 Caspase 9 caspase10 Caspase 10 chymotrypsin-high Chymotrypsin-high specificity (C-term to [FYW], not before P) chymotrypsin-low Chymotrypsin-low specificity (C-term to [FYWML], not before P) clostripain Clostripain (Clostridiopeptidase B) cnbr CNBr enterokinase Enterokinase factor xa Factor Xa formic acid Formic acid glutamyl endopeptidase Glutamyl endopeptidase granzyme-b Granzyme B hydroxylamine Hydroxylamine iodosobenzoic acid Iodosobenzoic acid lysc LysC lysn LysN neutrophil elastase Neutrophil elastase ntcb NTCB (2-nitro-5-thiocyanobenzoic acid) pepsin1.3 Pepsin (ph == 1.3) pepsin Pepsin (ph > 2) proline endopeptidase Proline-endopeptidase proteinase k Proteinase K staphylococcal peptidase i Staphylococcal Peptidase I thermolysin Thermolysin thrombin Thrombin trypsin Trypsin Value cleave If x is a character it returns a list of the same length as x. Each element contains a character vector with the corresponding cleavage products of the polypeptides. If x is an AAString or an AAStringSet an AAStringSet or an AAStringSetList instance of the same length as x is returned. Each element contains an AAString or an AAStringSet instance with the corresponding cleavage products of the polypeptides. cleavageranges If x is a character it returns a list of the same length as x. Each element contains a two-column matrix with the start and end positions of the peptides. If x is an AAString or an AAStringSet instance an IRanges or an IRangesList of the same length as x is returned. cleavagesites Returns a list of the same length as x. Each element contains an integer vector with the cleavage positions. Overview:
6 6 cleave Input cleave cleavageranges cleavagesites character list of character list of matrix list of integer AAString AAStringSet IRanges list of integer AAStringSet AAStringSetList IRangesList list of integer Author(s) Sebastian Gibb References Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A.; "Protein Identification and Analysis Tools on the ExPASy Server". (In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005). See Also AAString, AAStringSet, AAStringSetList, IRanges, IRangesList Examples library("cleaver") ## Gastric juice peptide 1 (UniProtKB/Swiss-Prot: GAJU_HUMAN/P01358) gaju <- "LAAGKVEDSD" cleave(gaju, "trypsin") # [1] "LAAGK" "VEDSD" cleavageranges(gaju, "trypsin") # [1,] 1 5 # [2,] 6 10 cleavagesites(gaju, "trypsin") # [1] 5 cleave(gaju, "trypsin", missedcleavages=1) # [1] "LAAGKVEDSD" cleavageranges(gaju, "trypsin", missedcleavages=1) # [1,] 1 10 cleave(gaju, "trypsin", missedcleavages=0:1) # [1] "LAAGK" "VEDSD" "LAAGKVEDSD" cleavageranges(gaju, "trypsin", missedcleavages=0:1)
7 cleave 7 # [1,] 1 5 # [2,] 6 10 # [3,] 1 10 cleave(gaju, "pepsin") # [1] "LAAGKVEDSD" # (no cleavage) ## use AAStringSet gaju <- AAStringSet("LAAGKVEDSD") cleave(gaju) # AAStringSetList of length 1 # [["LAAGKVEDSD"]] LAAGK VEDSD ## Beta-enolase (UniProtKB/Swiss-Prot: ENOB_THUAL/P86978) enob <- "SITKIKAREILD" cleave(enob, "trypsin") # [1] "SITK" "IK" "AR" "EILD" cleave(enob, "trypsin", missedcleavages=2) # [1] "SITKIKAR" "IKAREILD" cleave(enob, "trypsin", missedcleavages=0:2) # [1] "SITK" "IK" "AR" "EILD" "SITKIK" "IKAR" # [7] "AREILD" "SITKIKAR" "IKAREILD" ## define own cleavage rule: cleave at K cleave(enob, custom="k") # [1] "SITK" "IK" "AREILD" cleavageranges(enob, custom="k") # [1,] 1 4 # [2,] 5 6 # [3,] 7 12 ## define own cleavage rule: cleave at K but not if followed by A cleave(enob, custom=c("k", "K(?=A)")) # [1] "SITK" "IKAREILD" cleavageranges(enob, custom=c("k", "K(?=A)"))
8 8 cleave # [1,] 1 4 # [2,] 5 12 cleavagesites(enob, custom=c("k", "K(?=A)")) # [1] 4
9 Index Topic methods cleave, 2 Topic package cleaver-package, 2 AAString, 5, 6 AAStringSet, 5, 6 AAStringSetList, 5, 6 cleavageranges, 2 cleavageranges cleavageranges,aastring-method cleavageranges,aastringset-method cleavageranges,character-method cleavagesites, 2 cleavagesites cleavagesites,aastring-method (cleave), 2 cleavagesites,aastringset-method cleavagesites,character-method cleave, 2, 2 cleave,aastring-method cleave,aastringset-method cleave,character-method cleaver-package, 2 gregexpr, 3 IRanges, 5, 6 IRangesList, 5, 6 9
Package cleaver. August 2, 2013
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Version 0.2.0 Date 2016-12-13 Package skellam December 15, 2016 Title Densities and Sampling for the Skellam Distribution Author Jerry W. Lewis, Patrick E. Brown , Michail Tsagris
Package Metrics. November 3, 2017
Version 0.1.3 Title Evaluation Metrics for Machine Learning Package Metrics November 3, 2017 An implementation of evaluation metrics in R that are commonly used in supervised machine learning. It implements
Package bigtime. November 9, 2017
Package bigtime November 9, 2017 Type Package Title Sparse Estimation of Large Time Series Models Version 0.1.0 Author Ines Wilms [cre, aut], David S. Matteson [aut], Jacob Bien [aut], Sumanta Basu [aut]
Package photobiologyleds
Type Package Package photobiologyleds Title Spectral Data for Light-Emitting-Diodes Version 0.4.3-1 Date 2018-01-03 January 14, 2018 Maintainer Pedro J. Aphalo Spectral emission
Package face. January 19, 2018
Package face January 19, 2018 Title Fast Covariance Estimation for Sparse Functional Data Version 0.1-4 Author Luo Xiao [aut,cre], Cai Li [aut], William Checkley [aut], Ciprian Crainiceanu [aut] Maintainer
Package r2glmm. August 5, 2017
Type Package Package r2glmm August 5, 2017 Title Computes R Squared for Mixed (Multilevel) Models Date 2017-08-04 Version 0.1.2 The model R squared and semi-partial R squared for the linear and generalized
Package weathercan. July 5, 2018
Type Package Package weathercan July 5, 2018 Title Download Weather Data from the Environment and Climate Change Canada Website Version 0.2.7 Provides means for downloading historical weather data from
Package MAPA. R topics documented: January 5, Type Package Title Multiple Aggregation Prediction Algorithm Version 2.0.4
Type Package Title Multiple Aggregation Prediction Algorithm Version 2.0.4 Package MAPA January 5, 2018 Functions and wrappers for using the Multiple Aggregation Prediction Algorithm (MAPA) for time series
Package nowcasting. April 25, Type Package
Type Package Package nowcasting April 25, 2018 Title Nowcast Analysis and Create Real-Time Data Basis Version 0.1.3 Depends R (>= 3.4.0) Date 2018-04-25 Maintainer Daiane Marcolino de Mattos
Package MTA. R topics documented: May 14, Title Multiscalar Territorial Analysis Version 0.1.2
Title Multiscalar Territorial Analysis Version 0.1.2 Package MTA May 14, 2018 Build multiscalar territorial analysis based on various contexts. License GPL-3 URL https://github.com/riatelab/mta/ BugReports
Package survidinri. February 20, 2015
Package survidinri February 20, 2015 Type Package Title IDI and NRI for comparing competing risk prediction models with censored survival data Version 1.1-1 Date 2013-4-8 Author Hajime Uno, Tianxi Cai
Package effectfusion
Package November 29, 2016 Title Bayesian Effect Fusion for Categorical Predictors Version 1.0 Date 2016-11-21 Author Daniela Pauger [aut, cre], Helga Wagner [aut], Gertraud Malsiner-Walli [aut] Maintainer
Package sscor. January 28, 2016
Type Package Package sscor January 28, 2016 Title Robust Correlation Estimation and Testing Based on Spatial Signs Version 0.2 Date 2016-01-19 Depends pcapp, robustbase, mvtnorm Provides the spatial sign
Package factorqr. R topics documented: February 19, 2015
Package factorqr February 19, 2015 Version 0.1-4 Date 2010-09-28 Title Bayesian quantile regression factor models Author Lane Burgette , Maintainer Lane Burgette
Package RI2by2. October 21, 2016
Package RI2by2 October 21, 2016 Type Package Title Randomization Inference for Treatment Effects on a Binary Outcome Version 1.3 Author Joseph Rigdon, Wen Wei Loh, Michael G. Hudgens Maintainer Wen Wei
Package TSPred. April 5, 2017
Type Package Package TSPred April 5, 2017 Title Functions for Benchmarking Time Series Prediction Version 3.0.2 Date 2017-04-05 Author Rebecca Pontes Salles [aut, cre, cph] (CEFET/RJ), Eduardo Ogasawara
Package photobiologylamps
Type Package Package photobiologylamps Title Spectral Irradiance Data for Lamps Version 0.4.2 Date 2018-02-26 February 26, 2018 Maintainer Pedro J. Aphalo Spectral emission data