Merge branch 'develop'

Conflicts:
	R/charge.R

DESCRIPTION

@@ -1,11 +1,10 @@
 Package: Peptides
-Version: 1.0
-Date: 2014-08-30
+Version: 1.0.2
+Date: 2014-11-15
 Title: Calculate indices and theoretical physicochemical properties of peptides and protein sequences
 Author: Daniel Osorio, Paola Rondon-Villarreal and Rodrigo Torres.
 Maintainer: Daniel Osorio <[email protected]>
 URL: https://github.com/dosorio/Peptides/
-Depends: seqinr , R (>= 2.10.0)
 Suggests: RUnit
-Description: Calculate physicochemical properties and indices from aminoacid sequences of peptides and proteins. Include also utilities for read and plot GROMACS output files .XVG.
+Description: Calculate physicochemical properties and indices from aminoacid sequences of peptides and proteins. Include also utilities for read and plot GROMACS output files.
 License: GPL-2

NAMESPACE

@@ -1,2 +1 @@
 exportPattern("^[[:alpha:]]+")
-importFrom( seqinr, s2c )

R/AAcomp.R

@@ -10,7 +10,7 @@ aacomp<-function(seq){
   rownames(AA)<-c("Tiny","Small","Aliphatic","Aromatic","NonPolar","Polar","Charged","Basic","Acidic")
   colnames(AA)<-c("Number","Mole%")
   # Divide the amino acid sequence and makes a frequencies table
-  seq1<-table(s2c(toupper(seq)))
+  seq1<-table(strsplit(toupper(seq),"")[[1]])
   # Classify amino acids in a particular class and sum the absolute frequencies
   AA[1,1]<-sum(seq1[c("A","C","G","S","T")],na.rm = TRUE)
   AA[2,1]<-sum(seq1[c("A","B","C","D","G","N","P","S","T","V")],na.rm = TRUE)
@@ -23,6 +23,6 @@ aacomp<-function(seq){
   AA[9,1]<-sum(seq1[c("B","D","E","Z")],na.rm = TRUE)
   # Compute the relative frequencies for each class in percentage
   AA[,2]<-(AA[,1]/nchar(seq)*100)
-  # Return output matrix rounded to 2 decimals
-  return(round(AA,2))
+  # Return output matrix rounded to 3 decimals
+  return(round(AA,3))
 }

R/Boman.R

@@ -10,5 +10,5 @@ boman<-function(seq){
            H=-4.66, Q=-5.54, K=-5.55, N=-6.64, E=-6.81, D=-8.72, R=-14.92)
   # Asign a value to each amino acids in the sequence, sum the values and divide on amino acid sequence length
   # Report the index rounded to 2 decimals
-  round(-1*sum(boman[s2c(toupper(seq))],na.rm=T)/nchar(seq),2)
+  return(-1*sum(boman[strsplit(toupper(seq),"")[[1]]],na.rm=T)/nchar(seq))
 }

R/MW.R

@@ -10,7 +10,7 @@ mw<-function(seq){
             G=57.0519, H=137.1411, I=113.1594, L=113.1594, K=128.1741, M=131.1926, F=147.1766, 
             P=97.1167, S=87.0782,  T=101.1051, W=186.2132, Y=163.1760, V=99.1326,  U=150.0388, 
             O=237.3018)
-  # Sum the weight of each amino acid and add 18,2
+  # Sum the weight of each amino acid and add 18,02
   # Return the MW rounded to 2 decimals
-  round(sum(weight[s2c(toupper(seq))],na.rm=TRUE)+18.0153,2)
+  sum(weight[strsplit(toupper(seq),split = "")[[1]]],na.rm=TRUE)+18.0153
 }

R/aindex.R

@@ -5,7 +5,7 @@
 
 aindex<-function(seq){
   # Divide the amino acid sequence and extracts the relative frequency of Alanine, Valine, Leucine and Isoleucine
-  p<-(table(factor(s2c(toupper(seq)),levels = c("A","V","L","I")))/nchar(seq))
+  p<-table(strsplit(toupper(seq),"")[[1]])/nchar(seq)
 
   # Aliphatic index = X(Ala) + a * X(Val) + b * ( X(Ile) + X(Leu) )  
   # where X(Ala), X(Val), X(Ile), and X(Leu) are mole percent (100 X mole fraction) 

R/charge.R

@@ -4,13 +4,17 @@
 # The net charge can be calculated using one of the 9 pKa scales availables Bjellqvist, EMBOSS, Murray, Sillero, Solomon, 
 # Stryer, Lehninger, Dawson or Rodwell
 
+<<<<<<< HEAD
 charge <- function(seq,pH=7,pKscale= "Lehninger"){
+=======
+charge <- function(seq,pH=7,pKscale="EMBOSS"){
+>>>>>>> develop
   # # Divide the amino acid sequence and makes an absolute frequencies table
-  aa<-table(factor(prot<-s2c(toupper(seq)),levels = LETTERS))
+  aa<-table(factor(prot<-strsplit(toupper(seq),"")[[1]],levels = LETTERS))
   # Set pKscale
   data(pKscales, envir = environment())
   pKscales<-pKscales
-  pKs<-pKscales[,pmatch(pKscale,names(pKscales))]
+  pKs<-pKscales[,match.arg(pKscale,names(pKscales))]
   names(pKs) <- rownames(pKscales)
   # Charge
   cterm <- (-1 /(1+10^(-1*(pH-pKs["cTer"]))))

R/hmoment.R

@@ -3,30 +3,23 @@
 # The hydrophobic moment detects periodicity in protein hydrophobicity. 
 # Proceedings of the National Academy of Sciences of the United States of America, 81(1), 140–4.
 
-hmoment<-function(seq,angle){
-  # Loading Hydrophobicity scales
-  data(H, envir = environment())
-  # Setting global variables
-  H<-H
-  AA<-s2c(toupper(seq))
-  # Setting input length
-  if(nchar(seq)>10){
-    Pep<-NULL
-    for (i in 1: (nchar(seq)-9)){
-      Pep[i]<-paste(AA[i:(i+9)],collapse ="")}
-  }else{
-    Pep<-seq
-  }
-  # Defining the moment function
-  moment<-function(seq,angle){
-    vcos<-vsin<-uH<-NULL
-    aa<-s2c(toupper(seq))
-    for (i in 1: nchar(seq)){
-      vcos[i]<-(as.array(H[[12]])[aa[i]]*(cos((angle*(pi/180))*i)))
-      vsin[i]<-(as.array(H[[12]])[aa[i]]*(sin((angle*(pi/180))*i)))}
-    round(sqrt(sum(vcos,na.rm=TRUE)^2+sum(vsin,na.rm=TRUE)^2)/nchar(seq),2)
-  }
+hmoment<-function(seq,angle=100,window=11){
+  # Load hydrophobicity scale
+  data(H,envir = environment())
+  h<-H[["Eisenberg"]]
+  # Spliting the sequence
+  aa<-strsplit(toupper(seq),"")[[1]]
+  window<-min(length(aa),window)
+  # Setting the sequences
+  pep<-embed(aa,window)
+  # Evaluating angles and functions
+  angle<- angle*(pi/180)*1:window
+  vcos<-h[t(pep)]*cos(angle)
+  vsin<-h[t(pep)]*sin(angle)
+  dim(vcos)<-dim(vsin)<-dim(t(pep))
+  vcos<-colSums(vcos)
+  vsin<-colSums(vsin)
   # Applying the moment function to each 10 amino acids window
-  # Return the max value rounded to 3 decimals
-  max(sapply(Pep,function(x)moment(x,angle)))
+  # Return the max value
+  max(sqrt(vsin*vsin + vcos*vcos)/window)
 }

R/hydrophobicity.R

@@ -5,17 +5,17 @@
 # A simple method for displaying the hydropathic character of a protein. 
 # Journal of Molecular Biology, 157(1), 105–32.
 
-hydrophobicity<-function(seq,scale){
+hydrophobicity<-function(seq,scale="KyteDoolittle"){
   # Setting the hydrophobicity scale
   M<-c("KyteDoolittle","AbrahamLeo",   "BullBreese",   "Guy",          "Miyazawa",     "Roseman",      "Wolfenden",   
        "Wilson",       "Cowan3.4",     "Aboderin",     "Sweet",        "Eisenberg",    "HoppWoods",    "Manavalan",   
        "BlackMould",   "Fauchere",     "Janin",        "Rao",          "Tanford",      "Cowan7.5",     "Chothia",
        "Rose")
-  scale<-pmatch(scale,M)
+  scale<-match.arg(scale,M)
   # Loading hydrophobicity scales
   data(H, envir = environment())
   H<-H
   # Sum the hydrophobicity of each amino acid and divide them between the sequence length
-  # Return the GRAVY value rounded to 2 decimals
-  round(sum(H[[scale]][s2c(toupper(seq))],na.rm = TRUE)/nchar(seq),2)
+  # Return the GRAVY value
+  sum(H[[scale]][strsplit(seq,"")[[1]]])/nchar(seq)
 }

R/instaindex.R

@@ -32,13 +32,13 @@ instaindex<-function(seq){
                 AG=1,AA=1,AL=1,LW=24.68,LC=1,LM=1,LH=1,LY=1,LF=1,LQ=33.6,LN=1,LI=1,LR=20.26,LD=1,LP=20.26,LT=1,LK=-7.49,
                 LE=1,LV=1,LS=1,LG=1,LA=1,LL=1,"NA"=1)
   # Divide the amino acid sequence in dipeptides
-  dp<-NULL
-  AA<-s2c(toupper(seq))
+  dp<-character(nchar(seq)-1)
+  AA<-strsplit(toupper(seq),"")[[1]]
   for (i in 1: (nchar(seq)-1)){
     dp[i]<-paste(AA[i:(i+1)],collapse = "")
   }
   # Apply the formula:
   # (10/L)*sum(DIWV(XiYi+1) for each dipeptide)
   # Return the index value rounded to 2 decimals
-  round((10/nchar(seq))*sum(guruprasad[dp],na.rm = TRUE),2)
+  (10/nchar(seq))*sum(guruprasad[dp],na.rm = TRUE)
 }

R/membpos.R

@@ -3,37 +3,24 @@
 # Eisenberg, D. (1984). Three-dimensional structure of membrane and surface proteins. 
 # Annual Review of Biochemistry, 53, 595–623. doi:10.1146/annurev.bi.53.070184.003115
 
-membpos<-function(seq,angle){ 
+membpos<-function(seq,angle=100){ 
   # Setting input length
-  AA<-s2c(toupper(seq))
-  if(nchar(seq)>11){
-    Pep<-NULL
-    for (i in 1: (nchar(seq)-10)){
-      Pep[i]<-paste(AA[i:(i+10)],collapse ="")}
-  }else{
-    Pep<-toupper(seq)
+  aa<-strsplit(toupper(seq),"")[[1]]
+  window<-min(length(aa),11)
+  pep<-character(nchar(seq)-window)
+  for (i in 1: (nchar(seq)-window)){
+    pep[i]<-paste(aa[i:(i+window)],collapse = "")
   }
   # Compute the hmoment and hydrophobicity for each amino acid window
-  data<-NULL
-  data$Pep<-as.vector(Pep)
-  data$H<-as.vector(sapply(Pep,function(x)hydrophobicity(x,"Eisenberg")))
-  data$uH<-round(as.vector(sapply(Pep,function(x)hmoment(x,angle))),2)
-  data$m<-((-0.421*data$H)+0.579)
-
+  data<-as.data.frame(matrix(nrow = length(pep),ncol = 5))
+  data[,1]<-pep
+  data[,2]<-round(as.vector(sapply(pep,function(x)hydrophobicity(x,"Eisenberg"))),3)
+  data[,3]<-round(as.vector(sapply(pep,function(x)hmoment(x,angle,window))),3)
+  data[,4]<-(data[,2]*-0.421)+0.579
+  colnames(data)<-c("Pep","H","uH","m","MembPos")
   # Assigns a class depending on the hydrophobicity and hmoment
-  for (i in 1: length(Pep)){
-    if(data$uH[i]<=data$m[i] & data$H[i]>=0.5){
-      data$MembPos[i]<-"Transmembrane"
-    }else{
-      if (data$uH[i]<=data$m[i] & data$H[i]<=0.5){
-        data$MembPos[i]<-"Globular"
-      }
-      else{
-        if(data$uH[i]>=data$m[i]){
-          data$MembPos[i]<-"Surface"
-        }
-      }
-    }
-  }
-  return(as.data.frame(data[-4]))
+  data[which(data$uH<=data$m & data$H>=0.5),5]<-"Transmembrane"
+  data[which(data$uH<=data$m & data$H<=0.5),5]<-"Globular"
+  data[which(data$uH>=data$m),5]<-"Surface"
+  return(data[-4])
 }

R/pI.R

@@ -2,14 +2,13 @@
 # This function computes the theoretical pI of a protein sequence using one of the 9 pKa scales availables
 # Bjellqvist, EMBOSS, Murray, Sillero, Solomon, Stryer, Lehninger, Dawson or Rodwell
 
-pI<-function (seq,pKscale) 
+pI<-function (seq,pKscale="EMBOSS") 
 {
   # Define pH values
   pHs <- seq(0 , 14 , 0.001)
   # Evaluate the net charge for defined pHs
   charges <- charge(seq,pHs,pKscale)
   # Computes the pI and returns the value rounded to 3 decimals
-  I <- round(mean(pHs[which(abs(charges)==min(abs(charges)))]),3)
-  return(I)
+  return(pHs[which.min(abs(charges))])
 }
 

inst/tests/runit.boman.R

@@ -6,7 +6,7 @@ test.boman <- function(){
   # BOMAN INDEX  -1.24  
 
   # CHECK VALUES
-  checkEquals(boman("FLPVLAGLTPSIVPKLVCLLTKKC"),-1.24)
+  checkEquals(boman("FLPVLAGLTPSIVPKLVCLLTKKC"),-1.24,tolerance = 0.01)
 
   # CHECK OUTPUT CLASS
   checkTrue(is.numeric(boman("FLPVLAGLTPSIVPKLVCLLTKKC")))

inst/tests/runit.charge.R

@@ -8,9 +8,9 @@ test.charge <- function(){
   # COMPARED TO YADAMP
   # http://yadamp.unisa.it/showItem.aspx?yadampid=845&x=0,7055475
   # SEQUENCE: FLPVLAGLTPSIVPKLVCLLTKKC
-  checkEquals(round(charge("FLPVLAGLTPSIVPKLVCLLTKKC",5,pKscale = "Lehn"),1),3)
-  checkEquals(round(charge("FLPVLAGLTPSIVPKLVCLLTKKC",7,pKscale = "Lehn"),1),2.9)
-  checkEquals(round(charge("FLPVLAGLTPSIVPKLVCLLTKKC",9,pKscale = "Lehn"),1),1.0)
+  checkEquals(charge("FLPVLAGLTPSIVPKLVCLLTKKC",5,pKscale = "Lehn"),3,tolerance = 0.01)
+  checkEquals(charge("FLPVLAGLTPSIVPKLVCLLTKKC",7,pKscale = "Lehn"),2.9,tolerance = 0.01)
+  checkEquals(charge("FLPVLAGLTPSIVPKLVCLLTKKC",9,pKscale = "Lehn"),1.0,tolerance = 0.01)
 
   # CHECK OUTPUT CLASS
   checkTrue(is.numeric(charge("FLPVLAGLTPSIVPKLVCLLTKKC",7,pKscale = "Bjellqvist")))

inst/tests/runit.hmoment.R

@@ -6,10 +6,10 @@ test.hmoment <- function(){
   # BETA-SHEET  160º : 0.25
 
   # ALPHA HELIX VALUE
-  checkEquals(hmoment("FLPVLAGLTPSIVPKLVCLLTKKC",100), 0.56)
+  checkEquals(hmoment(seq = "FLPVLAGLTPSIVPKLVCLLTKKC",angle = 100,window = 11), 0.520,tolerance = 0.01)
 
   # BETA SHEET VALUE
-  checkEquals(hmoment("FLPVLAGLTPSIVPKLVCLLTKKC",160), 0.25)
+  checkEquals(hmoment(seq = "FLPVLAGLTPSIVPKLVCLLTKKC",angle = 160,window = 11), 0.271,tolerance = 0.01)  
 
   # CHECK OUTPUT CLASS
   checkTrue(is.numeric(hmoment("FLPVLAGLTPSIVPKLVCLLTKKC",100)))

inst/tests/runit.mw.R

@@ -4,7 +4,7 @@ mw.membpos <- function(){
   # SEQUENCE: QWGRRCCGWGPGRRYCVRWC 
 
   # CHECK MW VALUE
-  checkEquals(mw("QWGRRCCGWGPGRRYCVRWC"), 2485.91)
+  checkEquals(mw("QWGRRCCGWGPGRRYCVRWC"), 2485.91,tolerance = 0.01)
 
   # CHECK OUTPUT CLASS
   checkTrue(is.numeric(mw("QWGRRCCGWGPGRRYCVRWC")))

inst/tests/runit.pI.R

@@ -5,7 +5,7 @@ test.pI<- function(){
   # Theoretical pI: 9.88
 
   # CHECK pI VALUE
-  checkEquals(round(pI("QWGRRCCGWGPGRRYCVRWC","Bje"),2),9.88)
+  checkEquals(pI("QWGRRCCGWGPGRRYCVRWC","Bje"),9.88)
 
   # CHECK OUTPUT CLASS
   checkTrue(is.numeric(pI("QWGRRCCGWGPGRRYCVRWC","Bje")))

man/Pepdata.Rd

@@ -11,29 +11,29 @@ Physicochemical properties and indices from 100 amino acid sequences (50 antimic
 \format{
   A data frame with 100 observations on the following 23 variables.
   \describe{
-    \item{\code{Sequence}}{a character vector with the sequences of 100 peptides (50 antimicrobial and 50 non-antimicrobial)}
-    \item{\code{Group}}{Integrer vector with the group code \code{"0"} for non antimicrobial and \code{"1"} for antimicrobial}
-    \item{\code{Length}}{a numeric vector with the length of the amino acid sequence}
+    \item{\code{sequence}}{a character vector with the sequences of 100 peptides (50 antimicrobial and 50 non-antimicrobial)}
+    \item{\code{group}}{Integrer vector with the group code \code{"0"} for non antimicrobial and \code{"1"} for antimicrobial}
+    \item{\code{length}}{a numeric vector with the length of the amino acid sequence}
     \item{\code{mw}}{a numeric vector with the molecular weight of the amino acid sequence}
-    \item{\code{TinyAA}}{A numeric vector with the fraction (as percent) of tiny amino acids that make up the sequence}
-    \item{\code{SmallAA}}{A numeric vector with the fraction (as percent) of small amino acids that make up the sequence}
-    \item{\code{AliphaticAA}}{A numeric vector with the fraction (as percent) of aliphatic amino acids that make up the sequence}
-    \item{\code{AromaticAA}}{A numeric vector with the fraction (as percent) of aromatic amino acids that make up the sequence}
-    \item{\code{NonPolarAA}}{A numeric vector with the fraction (as percent) of non-polar amino acids that make up the sequence}
-    \item{\code{PolarAA}}{A numeric vector with the fraction (as percent) of polar amino acids that make up the sequence}
-    \item{\code{ChargedAA}}{A numeric vector with the fraction (as percent) of charged amino acids that make up the sequence}
-    \item{\code{BasicAA}}{A numeric vector with the fraction (as percent) of basic amino acids that make up the sequence}
-    \item{\code{AcidAA}}{A numeric vector with the fraction (as percent) of acid amino acids that make up the sequence}
+    \item{\code{tinyAA}}{A numeric vector with the fraction (as percent) of tiny amino acids that make up the sequence}
+    \item{\code{smallAA}}{A numeric vector with the fraction (as percent) of small amino acids that make up the sequence}
+    \item{\code{aliphaticAA}}{A numeric vector with the fraction (as percent) of aliphatic amino acids that make up the sequence}
+    \item{\code{aromaticAA}}{A numeric vector with the fraction (as percent) of aromatic amino acids that make up the sequence}
+    \item{\code{nonpolarAA}}{A numeric vector with the fraction (as percent) of non-polar amino acids that make up the sequence}
+    \item{\code{polarAA}}{A numeric vector with the fraction (as percent) of polar amino acids that make up the sequence}
+    \item{\code{chargedAA}}{A numeric vector with the fraction (as percent) of charged amino acids that make up the sequence}
+    \item{\code{basicAA}}{A numeric vector with the fraction (as percent) of basic amino acids that make up the sequence}
+    \item{\code{acidicAA}}{A numeric vector with the fraction (as percent) of acid amino acids that make up the sequence}
     \item{\code{charge}}{a numeric vector with the charge of the amino acid sequence}
     \item{\code{pI}}{a numeric vector with the isoelectric point of the amino acid sequence}
     \item{\code{aindex}}{a numeric vector with the aliphatic index of the amino acid sequence}
     \item{\code{instaindex}}{a numeric vector with the instability index of the amino acid sequence}
     \item{\code{boman}}{{a numeric vector with the potential peptide-interaction index of the amino acid sequence}}
-    \item{\code{h}}{{a numeric vector with the hydrophobicity index of the amino acid sequence}}
+    \item{\code{hydrophobicity}}{{a numeric vector with the hydrophobicity index of the amino acid sequence}}
     \item{\code{hmoment}}{a numeric vector with the hydrophobic moment of the amino acid sequence}
-    \item{\code{Transmembrane}}{A numeric vector with the fraction of Transmembrane windows of 11 amino acids that make up the sequence}
-    \item{\code{Surface}}{A numeric vector with the fraction of Surface windows of 11 amino acids that make up the sequence}
-    \item{\code{Globular}}{A numeric vector with the fraction of Globular windows of 11 amino acids that make up the sequence}
+    \item{\code{transmembrane}}{A numeric vector with the fraction of Transmembrane windows of 11 amino acids that make up the sequence}
+    \item{\code{surface}}{A numeric vector with the fraction of Surface windows of 11 amino acids that make up the sequence}
+    \item{\code{globular}}{A numeric vector with the fraction of Globular windows of 11 amino acids that make up the sequence}
   }
 }
 

man/Peptides-package.Rd

@@ -12,8 +12,8 @@ and proteins. Include also utilities for read and plot GROMACS output files .XVG
 \tabular{ll}{
 Package: \tab Peptides\cr
 Type: \tab Package\cr
-Version: \tab 1.0\cr
-Date: \tab 2014-08-30\cr
+Version: \tab 1.0.2\cr
+Date: \tab 2014-11-11\cr
 License: \tab GPL-2\cr
 }
 }

man/hmoment.Rd

@@ -8,12 +8,13 @@
 This function compute the hmoment based on Eisenberg, D., Weiss, R. M., & Terwilliger, T. C. (1984). Hydriphobic moment is a quantitative measure of the amphiphilicity perpendicular to the axis of any periodic peptide structure, such as the a-helix or b-sheet. It can be calculated for an amino acid sequence of N residues and their associated hydrophobicities Hn. If the secuence length is < 11 AA, the window length is equal to the AA sequence length, if it is > 11, windows of 11 residues are evaluated}
 
 \usage{
-hmoment(seq,angle)
+hmoment(seq,angle,window)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
-  \item{seq}{amino acid sequence as string}
+  \item{seq}{Amino acid sequence as string}
   \item{angle}{Protein rotational angle}
+  \item{window}{Sequence fraction length}
 }
 \value{
 The max hydrophobic moment (uH) as a numerical vector of length one}
@@ -24,14 +25,14 @@ Eisenberg, D., Weiss, R. M., & Terwilliger, T. C. (1984). The hydrophobic moment
 # COMPARED TO EMBOSS:HMOMENT
 # http://emboss.bioinformatics.nl/cgi-bin/emboss/hmoment
 # SEQUENCE: FLPVLAGLTPSIVPKLVCLLTKKC
-# ALPHA-HELIX ANGLE=100 : 0.56
-# BETA-SHEET  ANGLE=160 : 0.25
+# ALPHA-HELIX ANGLE=100 : 0.52
+# BETA-SHEET  ANGLE=160 : 0.271
 
 # ALPHA HELIX VALUE
-hmoment("FLPVLAGLTPSIVPKLVCLLTKKC",100)
-# [1] 0.56
+hmoment(seq = "FLPVLAGLTPSIVPKLVCLLTKKC",angle = 100, window = 11)
+# [1] 0.5199226
 
 # BETA SHEET VALUE
-hmoment("FLPVLAGLTPSIVPKLVCLLTKKC",160)
-# [1] 0.25
+hmoment(seq = "FLPVLAGLTPSIVPKLVCLLTKKC",angle = 160, window = 11)
+# [1] 0.2705906
 }