R/internaldbs.R

Defines functions getFormula dbFourChains dbThreeChains dbTwoChains dbOneChain dbSphingolipids MassCL MassTG MassDG MassMG MassPCo MassPCp MassPC MassLysoPCo MassLysoPCp MassLysoPC MassPS MassLysoPS MassPIP3 MassPIP2 MassPIP MassPI MassLysoPI MassPG MassLysoPG MassPEp MassPEo MassPE MassLysoPEp MassLysoPEo MassLysoPE MassPA MassLysoPAo MassLysoPA MassFAHFA MassHFA MassFA MassCE MassCarnitines MassSM MassGlcCer MassAcylCer MassCerP MassCer MassSphP MassSph

Documented in dbFourChains dbOneChain dbSphingolipids dbThreeChains dbTwoChains getFormula MassAcylCer MassCarnitines MassCE MassCer MassCerP MassCL MassDG MassFA MassFAHFA MassGlcCer MassHFA MassLysoPA MassLysoPAo MassLysoPC MassLysoPCo MassLysoPCp MassLysoPE MassLysoPEo MassLysoPEp MassLysoPG MassLysoPI MassLysoPS MassMG MassPA MassPC MassPCo MassPCp MassPE MassPEo MassPEp MassPG MassPI MassPIP MassPIP2 MassPIP3 MassPS MassSM MassSph MassSphP MassTG

# MassSph
#' Calculate formula and mass of sphingoid bases
#'
#' Calculate formula and mass of sphingoid bases
#'
#' @param Sph character value indicating total number of carbons and double
#' bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassSph <- function(Sph){
  cb <- unlist(strsplit(Sph, "[: ]"))
  C <- as.numeric(cb[1])
  H <- as.numeric(cb[1])*2+3-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO2"),
    collapse="")
  mass <- C*12+H*1.007825+14.00305+2*15.9949
  return(c(formula, mass))
}

# MassSphP
#' Calculate formula and mass of sphingoid phosphate bases
#'
#' Calculate formula and mass of sphingoid phosphate bases
#'
#' @param SphP character value indicating total number of carbons and double
#' bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassSphP <- function(SphP){
  cb <- unlist(strsplit(SphP, "[: ]"))
  C <- as.numeric(cb[1])
  H <- as.numeric(cb[1])*2+4-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO5P"),
                   collapse="")
  mass <- C*12+H*1.007825+14.00305+5*15.9949+30.97393
  return(c(formula, mass))
}

# MassCer
#' Calculate formula and mass of ceramides
#'
#' Calculate formula and mass of ceramides
#'
#' @param cer character value indicating total number of carbons and double
#' bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassCer <- function(cer){
  cb <- unlist(strsplit(cer, "[: ]"))
  C <- as.numeric(cb[1])
  H <- as.numeric(cb[1])*2+1-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO3"),
                   collapse="")
  mass <- C*12+H*1.007825+14.00305+3*15.9949
  return(c(formula, mass))
}

# MassCerP
#' Calculate formula and mass of ceramides phosphate
#'
#' Calculate formula and mass of ceramides phosphate
#'
#' @param cerP character value indicating total number of carbons and double
#' bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassCerP <- function(cerP){
  cb <- unlist(strsplit(cerP, "[: ]"))
  C <- as.numeric(cb[1])
  H <- as.numeric(cb[1])*2+2-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO6P"),
                   collapse="")
  mass <- C*12+H*1.007825+14.00305+6*15.9949+30.97393
  return(c(formula, mass))
}

# MassAcylCer
#' Calculate formula and mass of acylceramides
#'
#' Calculate formula and mass of acylceramides
#'
#' @param glccer character value indicating total number of carbons and double
#' bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassAcylCer <- function(acylcer){
  cb <- unlist(strsplit(acylcer, "[: ]"))
  C <- as.numeric(cb[1])
  H <- as.numeric(cb[1])*2-as.numeric(cb[2])*2-1
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO4"),
                   collapse="")
  mass <- C*12+H*1.007825+14.00305+4*15.9949
  return(c(formula, mass))
}

# MassGlcCer
#' Calculate formula and mass of glucoceramides
#'
#' Calculate formula and mass of glucoceramides
#'
#' @param glccer character value indicating total number of carbons and double
#' bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassGlcCer <- function(glccer){
  cb <- unlist(strsplit(glccer, "[: ]"))
  C <- as.numeric(cb[1])+6
  H <- as.numeric(cb[1])*2+11-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO8"),
                   collapse="")
  mass <- C*12+H*1.007825+14.00305+8*15.9949
  return(c(formula, mass))
}

# MassSM
#' Calculate formula and mass of sphingomyelines
#'
#' Calculate formula and mass of sphingomyelines
#'
#' @param SM character value indicating total number of carbons and double
#' bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassSM <- function(SM){
  cb <- unlist(strsplit(SM, "[: ]"))
  C <- as.numeric(cb[1])+5
  H <- as.numeric(cb[1])*2+13-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "N2O6P"),
                   collapse="")
  mass <- C*12+H*1.007825+2*14.00305+6*15.9949+30.97393
  return(c(formula, mass))
}

# MassCarnitines
#' Calculate formula and mass of carnitines
#'
#' Calculate formula and mass of carnitines
#'
#' @param carnitine character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassCarnitines <- function(carnitine){
  cb <- unlist(strsplit(carnitine, "[: ]"))
  C <- as.numeric(cb[1])+7
  H <- as.numeric(cb[1])*2+13-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO4"),
                   collapse="")
  mass <- C*12+H*1.007825++14.00305+4*15.9949
  return(c(formula, mass))
}

# MassCE
#' Calculate formula and mass of cholesterol esthers
#'
#' Calculate formula and mass of cholesterol esthers
#'
#' @param CE character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassCE <- function(CE){
  cb <- unlist(strsplit(CE, "[: ]"))
  C <- as.numeric(cb[1])+27
  H <- as.numeric(cb[1])*2+44-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O2"),
                   collapse="")
  mass <- C*12+H*1.007825+2*15.9949
  return(c(formula, mass))
}

# MassFA
#' Calculate formula and mass of fatty acids
#'
#' Calculate formula and mass of fatty acids
#'
#' @param FA character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassFA <- function(FA){
  cb <- unlist(strsplit(FA, "[: ]"))
  C <- as.numeric(cb[1])
  H <- as.numeric(cb[1])*2-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O2"),
                   collapse="")
  mass <- C*12+H*1.007825+2*15.9949
  return(c(formula, mass))
}

# MassHFA
#' Calculate formula and mass of hydroxi fatty acids
#'
#' Calculate formula and mass of hydroxi fatty acids
#'
#' @param HFA character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassHFA <- function(HFA){
  cb <- unlist(strsplit(HFA, "[: ]"))
  C <- as.numeric(cb[1])
  H <- as.numeric(cb[1])*2-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O3"),
                   collapse="")
  mass <- C*12+H*1.007825+3*15.9949
  return(c(formula, mass))
}

# MassFAHFA
#' Calculate formula and mass of FAHFA
#'
#' Calculate formula and mass of FAHFA
#'
#' @param FAHFA character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassFAHFA <- function(FAHFA){
  cb <- unlist(strsplit(FAHFA, "[: ]"))
  C <- as.numeric(cb[1])
  H <- as.numeric(cb[1])*2-2-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O4"),
                   collapse="")
  mass <- C*12+H*1.007825+4*15.9949
  return(c(formula, mass))
}

# MassLysoPA
#' Calculate formula and mass of LPA
#'
#' Calculate formula and mass of LPA
#'
#' @param LPA character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassLysoPA <- function(LPA){
  cb <- unlist(strsplit(LPA, "[: ]"))
  C <- as.numeric(cb[1])+3
  H <- as.numeric(cb[1])*2+7-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H),
                     "O7P"), collapse="")
  mass <- C*12+H*1.007825+7*15.9949+30.97393
  return(c(formula, mass))
}

# MassLysoPAo
#' Calculate formula and mass of LPAo
#'
#' Calculate formula and mass of LPAo
#'
#' @param LPAo character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassLysoPAo <- function(LPAo){
  cb <- unlist(strsplit(LPAo, "[: ]"))
  C <- as.numeric(cb[1])+3
  H <- as.numeric(cb[1])*2+9-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H),
                     "O6P"), collapse="")
  mass <- C*12+H*1.007825+6*15.9949+30.97393
  return(c(formula, mass))
}

# MassPA
#' Calculate formula and mass of PA
#'
#' Calculate formula and mass of PA
#'
#' @param PA character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassPA <- function(PA){
  cb <- unlist(strsplit(PA, "[: ]"))
  C <- as.numeric(cb[1])+3
  H <- as.numeric(cb[1])*2+5-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O8P"),
                   collapse="")
  mass <- C*12+H*1.007825+8*15.9949+30.97393
  return(c(formula, mass))
}

# MassLysoPE
#' Calculate formula and mass of LPE
#'
#' Calculate formula and mass of LPE
#'
#' @param LPE character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassLysoPE <- function(LPE){
  cb <- unlist(strsplit(LPE, "[: ]"))
  C <- as.numeric(cb[1])+5
  H <- as.numeric(cb[1])*2+12-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO7P"),
                   collapse="")
  mass <- C*12+H*1.007825+14.00305+7*15.9949+30.97393
  return(c(formula, mass))
}

# MassLysoPEo
#' Calculate formula and mass of LPEo
#'
#' Calculate formula and mass of LPEo
#'
#' @param LPEo character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassLysoPEo <- function(LPEo){
  cb <- unlist(strsplit(LPEo, "[: ]"))
  C <- as.numeric(cb[1])+5
  H <- as.numeric(cb[1])*2+14-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO6P"),
                   collapse="")
  mass <- C*12+H*1.007825+14.00305+6*15.9949+30.97393
  return(c(formula, mass))
}

# MassLysoPEp
#' Calculate formula and mass of LPEp
#'
#' Calculate formula and mass of LPEp
#'
#' @param LPEp character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassLysoPEp <- function(LPEp){
  cb <- unlist(strsplit(LPEp, "[: ]"))
  C <- as.numeric(cb[1])+5
  H <- as.numeric(cb[1])*2+12-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO6P"),
                   collapse="")
  mass <- C*12+H*1.007825+14.00305+6*15.9949+30.97393
  return(c(formula, mass))
}

# MassPE
#' Calculate formula and mass of PE
#'
#' Calculate formula and mass of PE
#'
#' @param PE character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassPE <- function(PE){
  cb <- unlist(strsplit(PE, "[: ]"))
  C <- as.numeric(cb[1])+5
  H <- as.numeric(cb[1])*2+10-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO8P"),
                   collapse="")
  mass <- C*12+H*1.007825+14.00305+8*15.9949+30.97393
  return(c(formula, mass))
}

# MassPEo
#' Calculate formula and mass of plasmanyl PE
#'
#' Calculate formula and mass of plasmanyl PE
#'
#' @param PEp character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassPEo <- function(PEo){
  cb <- unlist(strsplit(PEo, "[: ]"))
  C <- as.numeric(cb[1])+5
  H <- as.numeric(cb[1])*2+12-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO7P"),
                   collapse="")
  mass <- C*12+H*1.007825+14.00305+7*15.9949+30.97393
  return(c(formula, mass))
}

# MassPEp
#' Calculate formula and mass of plasmenyl PE
#'
#' Calculate formula and mass of plasmenyl PE
#'
#' @param PEp character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassPEp <- function(PEp){
  cb <- unlist(strsplit(PEp, "[: ]"))
  C <- as.numeric(cb[1])+5
  H <- as.numeric(cb[1])*2+10-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO7P"),
                   collapse="")
  mass <- C*12+H*1.007825+14.00305+7*15.9949+30.97393
  return(c(formula, mass))
}

# MassLysoPG
#' Calculate formula and mass of LPG
#'
#' Calculate formula and mass of LPG
#'
#' @param LPG character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassLysoPG <- function(LPG){
  cb <- unlist(strsplit(LPG, "[: ]"))
  C <- as.numeric(cb[1])+6
  H <- as.numeric(cb[1])*2+13-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H),
                     "O9P"), collapse="")
  mass <- C*12+H*1.007825+9*15.9949+30.97393
  return(c(formula, mass))
}

# MassPG
#' Calculate formula and mass of PG
#'
#' Calculate formula and mass of PG
#'
#' @param PG character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassPG <- function(PG){
  cb <- unlist(strsplit(PG, "[: ]"))
  C <- as.numeric(cb[1])+6
  H <- as.numeric(cb[1])*2+11-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H),
                     "O10P"), collapse="")
  mass <- C*12+H*1.007825+10*15.9949+30.97393
  return(c(formula, mass))
}

# MassLysoPI
#' Calculate formula and mass of LPI
#'
#' Calculate formula and mass of LPI
#'
#' @param LPI character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassLysoPI <- function(LPI){
  cb <- unlist(strsplit(LPI, "[: ]"))
  C <- as.numeric(cb[1])+9
  H <- as.numeric(cb[1])*2+17-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O12P"),
                   collapse="")
  mass <- C*12+H*1.007825+12*15.9949+30.97393
  return(c(formula, mass))
}

# MassPI
#' Calculate formula and mass of PI
#'
#' Calculate formula and mass of PI
#'
#' @param PI character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassPI <- function(PI){
  cb <- unlist(strsplit(PI, "[: ]"))
  C <- as.numeric(cb[1])+9
  H <- as.numeric(cb[1])*2+15-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O13P"),
                   collapse="")
  mass <- C*12+H*1.007825+13*15.9949+30.97393
  return(c(formula, mass))
}

# MassPIP
#' Calculate formula and mass of PIP
#'
#' Calculate formula and mass of PIP
#'
#' @param PIP character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassPIP <- function(PIP){
  cb <- unlist(strsplit(PIP, "[: ]"))
  C <- as.numeric(cb[1])+9
  H <- as.numeric(cb[1])*2+16-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O16P2"),
                   collapse="")
  mass <- C*12+H*1.007825+16*15.9949+2*30.97393
  return(c(formula, mass))
}

# MassPIP2
#' Calculate formula and mass of PIP2
#'
#' Calculate formula and mass of PIP2
#'
#' @param PIP2 character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassPIP2 <- function(PIP2){
  cb <- unlist(strsplit(PIP2, "[: ]"))
  C <- as.numeric(cb[1])+9
  H <- as.numeric(cb[1])*2+17-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O19P3"),
                   collapse="")
  mass <- C*12+H*1.007825+19*15.9949+3*30.97393
  return(c(formula, mass))
}

# MassPIP3
#' Calculate formula and mass of PIP3
#'
#' Calculate formula and mass of PIP3
#'
#' @param PIP3 character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassPIP3 <- function(PIP3){
  cb <- unlist(strsplit(PIP3, "[: ]"))
  C <- as.numeric(cb[1])+9
  H <- as.numeric(cb[1])*2+18-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O22P4"),
                   collapse="")
  mass <- C*12+H*1.007825+22*15.9949+4*30.97393
  return(c(formula, mass))
}

# MassLysoPS
#' Calculate formula and mass of LysoPS
#'
#' Calculate formula and mass of LysoPS
#'
#' @param LPS character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassLysoPS <- function(LPS){
  cb <- unlist(strsplit(LPS, "[: ]"))
  C <- as.numeric(cb[1])+6
  H <- as.numeric(cb[1])*2+12-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO9P"),
                   collapse="")
  mass <- C*12+H*1.007825+9*15.9949+30.97393+14.00305
  return(c(formula, mass))
}

# MassPS
#' Calculate formula and mass of PS
#'
#' Calculate formula and mass of PS
#'
#' @param PS character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassPS <- function(PS){
  cb <- unlist(strsplit(PS, "[: ]"))
  C <- as.numeric(cb[1])+6
  H <- as.numeric(cb[1])*2+10-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO10P"),
                   collapse="")
  mass <- C*12+H*1.007825+10*15.9949+30.97393+14.00305
  return(c(formula, mass))
}

# MassLysoPC
#' Calculate formula and mass of LysoPC
#'
#' Calculate formula and mass of LysoPC
#'
#' @param LPC character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassLysoPC <- function(LPC){
  cb <- unlist(strsplit(LPC, "[: ]"))
  C <- as.numeric(cb[1])+8
  H <- as.numeric(cb[1])*2+18-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO7P"),
                   collapse="")
  mass <- C*12+H*1.007825+7*15.9949+30.97393+14.00305
  return(c(formula, mass))
}

# MassLysoPCp
#' Calculate formula and mass of LysoPCp
#'
#' Calculate formula and mass of LysoPCp
#'
#' @param LPCp character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassLysoPCp <- function(LPCp){
  cb <- unlist(strsplit(LPCp, "[: ]"))
  C <- as.numeric(cb[1])+8
  H <- as.numeric(cb[1])*2+18-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO6P"),
                   collapse="")
  mass <- C*12+H*1.007825+6*15.9949+30.97393+14.00305
  return(c(formula, mass))
}

# MassLysoPCo
#' Calculate formula and mass of LysoPCo
#'
#' Calculate formula and mass of LysoPCo
#'
#' @param LPCo character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassLysoPCo <- function(LPCo){
  cb <- unlist(strsplit(LPCo, "[: ]"))
  C <- as.numeric(cb[1])+8
  H <- as.numeric(cb[1])*2+20-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO6P"),
                   collapse="")
  mass <- C*12+H*1.007825+6*15.9949+30.97393+14.00305
  return(c(formula, mass))
}

# MassPC
#' Calculate formula and mass of PC
#'
#' Calculate formula and mass of PC
#'
#' @param PC character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassPC <- function(PC){
  cb <- unlist(strsplit(PC, "[: ]"))
  C <- as.numeric(cb[1])+8
  H <- as.numeric(cb[1])*2+16-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO8P"),
                   collapse="")
  mass <- C*12+H*1.007825+8*15.9949+30.97393+14.00305
  return(c(formula, mass))
}

# MassPCp
#' Calculate formula and mass of PCp
#'
#' Calculate formula and mass of PCp
#'
#' @param PCp character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassPCp <- function(PCp){
  cb <- unlist(strsplit(PCp, "[: ]"))
  C <- as.numeric(cb[1])+8
  H <- as.numeric(cb[1])*2+16-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO7P"),
                   collapse="")
  mass <- C*12+H*1.007825+7*15.9949+30.97393+14.00305
  return(c(formula, mass))
}

# MassPCo
#' Calculate formula and mass of PCo
#'
#' Calculate formula and mass of PCo
#'
#' @param PCo character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassPCo <- function(PCo){
  cb <- unlist(strsplit(PCo, "[: ]"))
  C <- as.numeric(cb[1])+8
  H <- as.numeric(cb[1])*2+18-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "NO7P"),
                   collapse="")
  mass <- C*12+H*1.007825+7*15.9949+30.97393+14.00305
  return(c(formula, mass))
}

# MassMG
#' Calculate formula and mass of MG
#'
#' Calculate formula and mass of MG
#'
#' @param MG character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassMG <- function(MG){
  cb <- unlist(strsplit(MG, "[: ]"))
  C <- as.numeric(cb[1])+3
  H <- as.numeric(cb[1])*2+6-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O4"),
                   collapse="")
  mass <- C*12+H*1.007825+4*15.9949
  return(c(formula, mass))
}

# MassDG
#' Calculate formula and mass of DG
#'
#' Calculate formula and mass of DG
#'
#' @param DG character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassDG <- function(DG){
  cb <- unlist(strsplit(DG, "[: ]"))
  C <- as.numeric(cb[1])+3
  H <- as.numeric(cb[1])*2+4-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O5"),
                   collapse="")
  mass <- C*12+H*1.007825+5*15.9949
  return(c(formula, mass))
}

# MassTG
#' Calculate formula and mass of TG
#'
#' Calculate formula and mass of TG
#'
#' @param TG character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassTG <- function(TG){
  cb <- unlist(strsplit(TG, "[: ]"))
  C <- as.numeric(cb[1])+3
  H <- as.numeric(cb[1])*2+2-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O6"),
                   collapse="")
  mass <- C*12+H*1.007825+6*15.9949
  return(c(formula, mass))
}

# MassCL
#' Calculate formula and mass of CL
#'
#' Calculate formula and mass of CL
#'
#' @param CL character value indicating total number of carbons and
#' double bounds
#'
#' @return vector containing formula and mass
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
MassCL <- function(CL){
  cb <- unlist(strsplit(CL, "[: ]"))
  C <- as.numeric(cb[1])+9
  H <- as.numeric(cb[1])*2+14-as.numeric(cb[2])*2
  formula <- paste(c("C", as.character(C), "H", as.character(H), "O17P2"),
                   collapse="")
  mass <- C*12+H*1.007825+17*15.9949+2*30.97393
  return(c(formula, mass))
}

# dbSphingolipids
#' Creation of a database for Cer, CerP, GlcCer and SM
#'
#' Creation of a database for Cer, CerP, GlcCer and SM
#'
#' @param chains character vector indicating the FAs to be employed
#' @param chains2 character vector indicating the sphingoid bases to be employed
#' @param lipid character value indication the class of lipid.
#'
#' @return data frame containing formula, mass and total number of carbons and
#' insaturations.
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
dbSphingolipids <- function(chains, chains2, lipid){
  comb <- vector()
  if (lipid == "AcylCer"){
    comb1 <- unique(utils::combn(chains, 2, simplify=F))
    chains <- unique(unlist(lapply(comb1, paste, collapse=" ")))
    for (i in chains2){
      comb <- append(comb, sapply(chains, paste, i, collapse=" "))
    }
    total  <- unique(unlist(lapply(comb, sumChains, n = 3)))
  } else {
    for (i in chains2){
      comb <- append(comb, sapply(chains, paste, i, collapse=" "))
    }
    comb <- unique(comb)
    total  <- unique(unlist(lapply(comb, sumChains, n = 2)))
  }
  if (lipid == "Cer"){
    fm <- lapply(total, MassCer)
  } else if (lipid == "GlcCer"){
    fm <- lapply(total, MassGlcCer)
  } else if (lipid == "CerP"){
    fm <- lapply(total, MassCerP)
  } else if (lipid == "SM"){
    fm <- lapply(total, MassSM)
  } else if (lipid == "AcylCer"){
    fm <- lapply(total, MassAcylCer)
  }
  db <- data.frame(formula=unlist(lapply(fm, "[[", 1)), total=total,
                   Mass=as.numeric(unlist(lapply(fm, "[[", 2))), stringsAsFactors = F)
  return(db)
}

# dbOneChain
#' Creation of a database for Carnitines, CE, FA, HFA, LPL, MG, sphingoid
#' bases and sphingoid bases phosphate.
#'
#' Creation of a database for Carnitines, CE, FA, HFA, LPL, MG, sphingoid
#' bases and sphingoid bases phosphate.
#'
#' @param chains character vector indicating the FAs to be employed
#' @param lipid character value indication the class of lipid.
#'
#' @return data frame containing formula, mass and total number of carbons and
#' insaturations
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
dbOneChain <- function(chains, lipid){
  fas <- unique(chains)
  if (lipid == "Carnitine"){
    fm <- lapply(fas, MassCarnitines)
  } else if (lipid == "CE"){
    fm <- lapply(fas, MassCE)
  } else if (lipid == "FA"){
    fm <- lapply(fas, MassFA)
  } else if (lipid == "HFA"){
    fm <- lapply(fas, MassHFA)
  } else if(lipid == "LPA"){
    fm <- lapply(fas, MassLysoPA)
  } else if(lipid == "LPE"){
    fm <- lapply(fas, MassLysoPE)
  } else if(lipid == "LPG"){
    fm <- lapply(fas, MassLysoPG)
  } else if(lipid == "LPI"){
    fm <- lapply(fas, MassLysoPI)
  } else if(lipid == "LPS"){
    fm <- lapply(fas, MassLysoPS)
  } else if(lipid == "LPC"){
    fm <- lapply(fas, MassLysoPC)
  } else if(lipid == "MG"){
    fm <- lapply(fas, MassMG)
  } else if(lipid == "Sph"){
    fm <- lapply(fas, MassSph)
  } else if(lipid == "SphP"){
    fm <- lapply(fas, MassSphP)
  } else if(lipid == "LPCo"){
    fm <- lapply(fas, MassLysoPCo)
  } else if(lipid == "LPCp"){
    fm <- lapply(fas, MassLysoPCp)
  } else if(lipid == "LPEo"){
    fm <- lapply(fas, MassLysoPEo)
  } else if(lipid == "LPEp"){
    fm <- lapply(fas, MassLysoPEp)
  } else if(lipid == "LPAo"){
    fm <- lapply(fas, MassLysoPAo)
  }
  db <- data.frame(formula=unlist(lapply(fm, "[[", 1)), total=fas,
                   Mass=as.numeric(as.vector(unlist(lapply(fm, "[[", 2)))),
                   stringsAsFactors = F)
  return(db)
}

# dbTwoChains
#' Creation of a database for FAHFA, DG and PL.
#'
#' Creation of a database for FAHFA, DG and PL.
#'
#' @param chains character vector indicating the FAs to be employed
#' @param lipid character value indication the class of lipid.
#'
#' @return data frame containing formula, mass and total number of carbons and
#' insaturations
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
dbTwoChains <- function(chains, lipid){
  fas <- rep(chains, 2)
  comb <- unique(utils::combn(fas, 2, simplify=F))
  total  <- unique(unlist(lapply(comb, sumChains, n = 2)))
  if (lipid == "PE"){
    fm <- lapply(total, MassPE)
  } else if (lipid == "PG"){
    fm <- lapply(total, MassPG)
  } else if (lipid == "PI"){
    fm <- lapply(total, MassPI)
  } else if (lipid == "PIP"){
    fm <- lapply(total, MassPIP)
  } else if (lipid == "PIP2"){
    fm <- lapply(total, MassPIP2)
  } else if (lipid == "PIP3"){
    fm <- lapply(total, MassPIP3)
  } else if (lipid == "PC"){
    fm <- lapply(total, MassPC)
  } else if (lipid == "DG"){
    fm <- lapply(total, MassDG)
  } else if (lipid == "FAHFA"){
    fm <- lapply(total, MassFAHFA)
  } else if (lipid == "PS"){
    fm <- lapply(total, MassPS)
  } else if (lipid == "PA"){
    fm <- lapply(total, MassPA)
  } else if (lipid == "PCo"){
    fm <- lapply(total, MassPCo)
  } else if (lipid == "PCp"){
    fm <- lapply(total, MassPCp)
  } else if (lipid == "PEo"){
    fm <- lapply(total, MassPEo)
  } else if (lipid == "PEp"){
    fm <- lapply(total, MassPEp)
  }
  db <- data.frame(formula=unlist(lapply(fm, "[[", 1)), total=total,
                   Mass=as.numeric(as.vector(unlist(lapply(fm, "[[", 2)))),
                   stringsAsFactors = F)
  return(db)
}

# dbThreeChains
#' Creation of a database for TG.
#'
#' Creation of a database for TG.
#'
#' @param chains character vector indicating the FAs to be employed
#' @param lipid character value indication the class of lipid.
#'
#' @return data frame containing formula, mass and total number of carbons and
#' insaturations
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
dbThreeChains <- function(chains, lipid){
  fas <- rep(chains, 3)
  comb <- unique(utils::combn(fas, 3, simplify=F))
  total  <- unique(unlist(lapply(comb, sumChains, n = 3)))
  if (lipid == "TG"){
    fm <- lapply(total, MassTG)
  }
  db <- data.frame(formula=unlist(lapply(fm, "[[", 1)), total=total,
                   Mass=as.numeric(as.vector(unlist(lapply(fm, "[[", 2)))),
                   stringsAsFactors = F)
  return(db)
}

# dbFourChains
#' Creation of a database for C.
#'
#' Creation of a database CL.
#'
#' @param chains character vector indicating the FAs to be employed
#' @param lipid character value indication the class of lipid.
#'
#' @return data frame containing formula, mass and total number of carbons and
#' insaturations
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
dbFourChains <- function(chains, lipid){
  fas <- rep(chains, 4)
  comb <- unique(utils::combn(fas, 4, simplify=F))
  total  <- unique(unlist(lapply(comb, sumChains, n = 4)))
  if (lipid == "CL"){
    fm <- lapply(total, MassCL)
  }
  db <- data.frame(formula=unlist(lapply(fm, "[[", 1)), total=total,
                   Mass=as.numeric(as.vector(unlist(lapply(fm, "[[", 2)))),
                   stringsAsFactors = F)
  return(db)
}

# getFormula
#' Get formula and neutral mass for annotated compounds
#'
#' Get formula and neutral mass for annotated compounds.
#'
#' @param df data frame with the input results
#' @param dbs list of data bases required for annotation. By default, dbs
#' contains the required data frames based on the default fragmentation rules.
#' If these rules are modified, dbs may need to be supplied. See \link{createLipidDB}
#' and \link{assignDB}.
#'
#' @return Data frame
#'
#' @keywords internal
#'
#' @author M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
getFormula <- function(df, dbs){
  lipidClass <- df["Class"]
  cdb <- df["CDB"]
  if (missing(dbs)){
    dbs <- assignDB()
  }
  if (lipidClass == "BA"){
    db <- dbs$badb
  } else if (lipidClass == "Carnitine"){
    db <- dbs$carnitinesdb
  } else if (lipidClass == "Cer"){
    db <- dbs$cerdb
  } else if (lipidClass == "CL"){
    db <- dbs$cldb
  } else if (lipidClass == "DG"){
    db <- dbs$dgdb
  } else if (lipidClass == "CE"){
    db <- dbs$CEdb
  } else if (lipidClass == "FA"){
    db <- dbs$fadb
  } else if (lipidClass == "FAHFA"){
    db <- dbs$fahfadb
  } else if (lipidClass == "HFA"){
    db <- dbs$hfadb
  } else if (lipidClass == "LPC"){
    db <- dbs$lysopcdb
  } else if (lipidClass == "LPE"){
    db <- dbs$lysopedb
  } else if (lipidClass == "LPG"){
    db <- dbs$lysopgdb
  } else if (lipidClass == "LPI"){
    db <- dbs$lysopidb
  } else if (lipidClass == "LPS"){
    db <- dbs$lysopsdb
  } else if (lipidClass == "MG"){
    db <- dbs$mgdb
  } else if (lipidClass == "PC"){
    db <- dbs$pcdb
  } else if (lipidClass == "PE"){
    db <- dbs$pedb
  } else if (lipidClass == "PG"){
    db <- dbs$pgdb
  } else if (lipidClass == "PI"){
    db <- dbs$pidb
  } else if (lipidClass == "PS"){
    db <- dbs$psdb
  } else if (lipidClass == "SM"){
    db <- dbs$smdb
  } else if (lipidClass == "Sph"){
    db <- dbs$sphdb
  } else if (lipidClass == "SphP"){
    db <- dbs$sphPdb
  } else if (lipidClass == "TG"){
    db <- dbs$tgdb
  } else if (lipidClass == "TG"){
    db <- dbs$tgdb
  } else if (lipidClass == "PCo"){
    db <- dbs$pcodb
  } else if (lipidClass == "PCp"){
    db <- dbs$pcpdb
  } else if (lipidClass == "PEo"){
    db <- dbs$peodb
  } else if (lipidClass == "PEp"){
    db <- dbs$pepdb
  } else if (lipidClass == "LPCo"){
    db <- dbs$lysopcodb
  } else if (lipidClass == "LPCp"){
    db <- dbs$lysopcpdb
  } else if (lipidClass == "LPEo"){
    db <- dbs$lysopeodb
  } else if (lipidClass == "LPEp"){
    db <- dbs$lysopepdb
  } else if (lipidClass == "CerP"){
    db <- dbs$cerPdb
  } else if (lipidClass == "AcylCer"){
    db <- dbs$acylcerdb
  }
  index <- which(db$total == as.character(cdb))
  if(length(index) > 0){
    formula <- db$formula[index]
    Mn <- db$Mass[index]
  } else {
    tempdb <- createLipidDB(lipidClass,
                            chains = c(as.character(cdb),
                                       "0:0", "0:0", "0:0"),
                            chains2 = "0:0")[[1]]
    formula <- tempdb[tempdb$total == as.character(cdb), 1]
    Mn <- tempdb[tempdb$total == as.character(cdb), 3]
  }
  return(data.frame(Formula = as.character(formula),
                    Mn = as.numeric(Mn), stringsAsFactors = FALSE))
}

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LipidMS documentation built on July 7, 2021, 9:07 a.m.