Merge pull request #2 from jasenfinch/tidy

Tidy

.Rbuildignore

@@ -1,5 +1,10 @@
-^.*\.Rproj$
-^\.Rproj\.user$
+mzAnnotation.Rproj
+.Rproj.user
 .travis.yml
 appveyor.yml
-README.md
+README.md
+.gitignore
+.git
+.Rhistory
+^.*\.Rproj$
+^\.Rproj\.user$

.travis.yml

@@ -7,21 +7,15 @@ warnings_are_errors: true
 apt_packages:
  - default-jre
  - default-jdk
- - libnetcdf-dev
- - udunits-bin
- - libudunits2-dev
 
 r_binary_packages:
  - RUnit
  - testthat
 
 bioc_packages:
- - mzR
- - CAMERA
-
+ - survival
+
 r_github_packages:
- - jasenfinch/binneR
- - jasenfinch/mzAnnotation
  - jasenfinch/cdkr/rcdk
 
 notifications:

DESCRIPTION

@@ -1,21 +1,13 @@
 Package: mzAnnotation
 Type: Package
-Title: Signal annotation tools for FIE-HRMS metabolomics
-Version: 1.0
-Date: 2015-03-29
+Title: Signal annotation tools for high resolution metabolomics
+Version: 1.1.0
+Date: 2016-11-11
 Author: Jasen Finch
 Maintainer: Jasen Finch <[email protected]>
-Description: More about what it does (maybe more than one line)
-License: What license is it under?
-Imports:
-    Rcpp (>= 0.11.0)
+Description: Tools for the putative annotation of high resolution metabolomics data.
+License: GPL (>= 2)
+Imports: Rcpp, plyr, shiny, rcdk, graphics, DT
 LinkingTo: Rcpp
-Depends:
-    Hmisc,
-    plyr,
-    shiny,
-    rcdk,
-    mzR,
-    binneR,
-    CAMERA
 RoxygenNote: 5.0.1
+LazyData: true

NAMESPACE

@@ -1,25 +1,33 @@
 # Generated by roxygen2: do not edit by hand
 
-export(annotSheet)
-export(annotateFIE)
-export(annotateLC)
-export(calcDiff)
-export(corAnalysis)
-export(corAnalysisLC)
-export(corLists)
-export(filterIso)
-export(filterMF)
-export(filterPIP)
-export(getIsoDist)
-export(getMF)
-export(getPIP)
+export(PIPsearch)
+export(generateMF)
 export(isoDistr)
-export(makeTable)
-export(mfGen)
-export(queryPIP)
+export(relationshipPredictor)
 export(shinyMZedDB)
-export(viewAnnotation)
-export(viewAnnotationLC)
-import(Hmisc)
+importFrom(DT,dataTableOutput)
+importFrom(DT,renderDataTable)
 importFrom(Rcpp,evalCpp)
+importFrom(graphics,par)
+importFrom(graphics,plot)
+importFrom(graphics,rasterImage)
+importFrom(plyr,ldply)
+importFrom(rcdk,parse.smiles)
+importFrom(rcdk,view.image.2d)
+importFrom(shiny,checkboxInput)
+importFrom(shiny,column)
+importFrom(shiny,fluidRow)
+importFrom(shiny,mainPanel)
+importFrom(shiny,navbarPage)
+importFrom(shiny,numericInput)
+importFrom(shiny,plotOutput)
+importFrom(shiny,reactive)
+importFrom(shiny,renderPlot)
+importFrom(shiny,renderTable)
+importFrom(shiny,shinyApp)
+importFrom(shiny,sidebarPanel)
+importFrom(shiny,tabPanel)
+importFrom(shiny,tableOutput)
+importFrom(shiny,textInput)
+importFrom(utils,combn)
 useDynLib(mzAnnotation)

R/PIPsearch.R

@@ -0,0 +1,52 @@
+#' Putative Ionisation Product searching
+#' @param mz the accurate m/z to search
+#' @param mode either 'p' or 'n' specifiying the acquisition mode
+#' @param ppm the parts per million threshold to search
+#' @param add a character \code{vector} specifying the adducts to search. If \code{NULL} a default selection will be used.
+#' @param iso a character \code{vector} specifying the isotopes to search. If \code{NULL} isotopes will not be searched.
+#' @details The underlying database is that of MZedDB (\url{http://maltese.dbs.aber.ac.uk:8888/hrmet/index.html}). 
+#' A list of available adducts can be found at \url{http://maltese.dbs.aber.ac.uk:8888/hrmet/search/disprules.php}. 
+#' Isotopic adducts have also been added and include [2M+K41]1+, [M+K41]1+, [M+K41-2H]1- and [M+Cl37]1-. 
+#' Available isotopes include C13, 2C13, 3C13, 4C13, O18, Cl37, K41 and S34.
+#' @export
+#' @author  Jasen Finch
+#' @importFrom plyr ldply
+#' @examples
+#' res <- PIPsearch(133.01378,'n',5)
+
+PIPsearch <-
+function(mz,mode,ppm,add = NULL, iso = NULL){
+  if (is.null(add)) {
+	  if (mode == "p" & is.null(add)) {
+				  adducts <- c("[M+2Na]2+","[M+H+K]2+","[M+H+Na]2+","[M+H+NH4]2+","[M+2H]2+","[M+2H-H2O-NH3]2+","[2M+K]1+","[2M+K41]1+","[2M+Na]1+","[2M+NH4]1+",
+				         "[2M+H]1+","[M+2K-H]1+","[M+2Na-H]1+","[M+K]1+","[M+K41]1+","[M+K41]1+","[M+Na]1+","[M+H]1+","[M1+.]1+","[M+H-NH3]1+","[M+H-H2O]1+",
+				         "[M+H-FA]1+")
+	  }
+	  if (mode == "n" & is.null(add)) {
+		  	adducts <- c("[2M+Na-2H]1-","[2M-H]1-","[M+K-2H]1-","[M+K41-2H]1-","[M+Cl]1-",'[M+Cl37]1-',"[M+Na-2H]1-","[M1-.]1-","[M-H]1-","[M-2H]2-")
+	  }
+    if (mode == "ne") {
+      adducts <- c("M") 
+    }
+  } else {
+    adducts <- add
+  }
+  if (!is.null(iso)) {
+    iso <- c('',iso)
+  } else {
+    iso <- ''
+  }
+
+	## Loop over adducts irrespective of isotopes
+	res <- lapply(iso,function(iso,adducts,mz,ppm,bio){
+	  if (iso == '') {
+	    iso <- NULL
+	  }
+	  lapply(adducts,queryPIP,mz = mz,ppm = ppm,iso = iso)
+	  },adducts = adducts,mz = mz,ppm = ppm)
+	res <- lapply(res,ldply,stringsAsFactors = F)
+	res <- ldply(res,stringsAsFactors = F)
+	names(res) <- c("ID","Name","MF","Accurate Mass","Smiles","Adduct",'Isotope',"Adduct m/z","PPM Error")
+
+	return(res)
+}

R/RcppExports.R

@@ -1,7 +1,6 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-#' @export
 mfGen <- function(measured_mass, max, min, tolerance, charge, applygr) {
     .Call('mzAnnotation_mfGen', PACKAGE = 'mzAnnotation', measured_mass, max, min, tolerance, charge, applygr)
 }

R/filterPIP.R

@@ -0,0 +1,14 @@
+
+filterPIP <- 
+  function(res){
+    patterns <- c("ic acid","keto","<i>","</i>","(R)-","(S)-","-L-","L-","(+)-",
+                  "cis,","cis-","trans-","&beta;-","-D-",
+                  "D-","D.","&gamma;-","-n-","N-","&alpha;-","&alpha;","&beta;")
+    replacements <- c("ate","oxo","","","","","","","","","","","","","","","","","","","","")
+    for (i in 1:length(patterns)) {
+      res[,2] <- sapply(res[,2],gsub,pattern = patterns[i],replacement = replacements[i],fixed = TRUE)
+    }
+    res[,2] <- tolower(res[,2])
+    res <- res[!duplicated(res[,2]),]
+    return(res)
+  }

R/generateMF.R

@@ -0,0 +1,32 @@
+#' Molecular formula generation
+#' @param mz accurate m/z for MF generation
+#' @param ppm ppm tolerance for MF generation
+#' @param charge charge to apply to MF generation
+#' @param applygr \code{boolean} denoting whether to apply the 7 golden rules
+#' @param composition numeric \code{vector} of maximum elemental composition
+#' @details Uses the HR2 molecular formula generator available at \url{http://maltese.dbs.aber.ac.uk:8888/hrmet/supp/rhrmet.html}.
+#' @author Jasen Finch
+#' @export
+#' @return A \code{data.frame} containing the generated MFs, their theoretical m/z and their PPM error.
+#' @examples
+#' res <- generateMF(341.10894,ppm = 5,charge = -1, applygr = TRUE,
+#'              composition=c(C = 12,iC = 0,H = 22,iH = 0,N = 0,iN = 0,O = 11,iO = 0,F = 0 ,Na = 0,
+#'                    Si = 0,P = 0,S = 0,Cl = 0,iCl = 0,Br = 0,iBr = 0,K = 0,iK = 0))
+
+generateMF <- function(mz, ppm = 5, charge = 0, applygr = TRUE, composition = c(C = 12,iC = 0,H = 22,iH = 0,N = 0,iN = 0,O = 11,iO = 0,
+                                                         F = 0 ,Na = 0,Si = 0,P = 0,S = 0,Cl = 0,iCl = 0,Br = 0,
+                                                         iBr = 0,K = 0,iK = 0)){
+    mmu <- ppm/10^6*mz*1000
+    res <- mfGen(mz,composition,rep(0,19),mmu,charge,applygr)	
+
+    if (length(res) == 0) {
+      res <- data.frame(matrix(nrow = 0,ncol = 3))
+      colnames(res) <- c("MF", "m/z", "PPM Error")
+    } else{
+      res <- data.frame(matrix(unlist(res), nrow = length(res),byrow = T),stringsAsFactors = F)
+      res <- res[,-c(1,3,5)]
+      colnames(res) <- c("MF", "m/z","PPM Error")
+      res[,3] <- sapply(as.numeric(as.character(res[,2])),function(x,mass){x <- as.numeric(x);x <- (x - mass)/mass*10^6; return(round(x,5))},mass = mz)
+    } 
+    return(res)
+  }