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-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/MFAssignAll_MSMS.R
-\name{MFAssignAll_MSMS}
-\alias{MFAssignAll_MSMS}
-\title{Assigns all possible MF to each row of input data frame with CHOFIT algorithm}
-\usage{
-MFAssignAll_MSMS(peaks, isopeaks = "none", ionMode, lowMW = 100,
-  highMW = 1000, POEx = 0, NOEx = 0, Nx = 0, Sx = 0, Px = 0,
-  S34x = 0, N15x = 0, Dx = 0, Ex = 0, Clx = 0, Fx = 0, Cl37x = 0,
-  Mx = 0, NH4x = 0, Zx = 1, Ox = 30, ppm_err = 3, SN = 0,
-  O_Cmin = 0, O_Cmax = 2.5, H_Cmin = 0.3, H_Cmax = 3, DBEOmin = -13,
-  DBEOmax = 13, Omin = 0, HetCut = "off", NMScut = "on")
-}
-\arguments{
-\item{peaks}{data frame, Monoisotopic Masses}
-
-\item{isopeaks}{data frame, Isotopic Masses. Default is "none"}
-
-\item{ionMode}{string: ("neg", "pos")}
-
-\item{lowMW}{numeric:
-Sets the lower limit of molecular mass to be assigned. Default is 100.}
-
-\item{highMW}{numeric:
-Sets the upper limit of molecular mass to be assigned. Default is 1000.}
-
-\item{POEx}{numeric:
-If set to 1 and ionMode is positive, positive mode odd electron ions can be assigned.
-Default is 0}
-
-\item{NOEx}{numeric:
-If set to 1 and ionMode is negative, negative mode odd electron ions can be assigned.
-Default is 0}
-
-\item{Nx}{numeric:
-Sets the maximum allowable number of Nitrogen 14 to be used in assignment. Default is 0.}
-
-\item{Sx}{numeric:
-Sets the maximum allowable number of Sulfur 32 to be used in assignment. Default is 0.}
-
-\item{Px}{numeric:
-Sets the maximum allowable number of Phosphorus 31 to be used in assignment. Default is 0.}
-
-\item{S34x}{numeric:
-Sets the amount of Sulfur 34 to be used in assignment. Default is 0.}
-
-\item{N15x}{numeric:
-Sets the amount of Nitrogen 15 to be used in assignment. Default is 0.}
-
-\item{Dx}{numeric:
-Sets the amount of Deuterium to be used in assignment. Default is 0.}
-
-\item{Ex}{numeric:
-Sets the amount of Carbon 13 to be used in assignment. Default is 0.}
-
-\item{Clx}{numeric:
-Sets the amount of Chlorine to be used in assignment. Default is 0.
- @param Fx numeric:
-Sets the amount of Fluorine to be used in assignment. Default is 0.}
-
-\item{Cl37x}{numeric:
-Sets the amount of Chlorine 37 to be used in assignment. Default is 0.}
-
-\item{Mx}{numeric:
-Sets the amount of Sodium adduct to be used in assignment. Default is 0.}
-
-\item{NH4x}{numeric:
-Sets the amount of Ammonium adduct to be used in assignment. Default is 0.}
-
-\item{Zx}{numeric:
-Sets the amount of charge to be used in assignment. Default is 1.}
-
-\item{Ox}{numeric:
-Ox sets the maximum number of oxygen looked for in the CHOFIT core, it limits the number of loops performed}
-
-\item{ppm_err}{numeric:
-ppm_err parameter sets the error tolerance (ppm) for formula assignment. Default is 3.}
-
-\item{SN}{numeric:
-SN parameter set the signal to noise cut for formula assignment. Default is 0.}
-
-\item{O_Cmin}{numeric:
-O_Cmin parameter sets the minimum allowed oxygen to carbon ratio. Default is 0.}
-
-\item{O_Cmax}{numeric:
-The O_Cmax parameter sets the upper limit for oxygen to carbon ratio. Default is 2.5.}
-
-\item{H_Cmin}{numeric:
-H_Cmin parameter sets lower limit for hydrogen to carbon ratio. Default is 0.1.}
-
-\item{H_Cmax}{numeric:
-H_Cmax parameter sets upper limit for hydrogen to carbon ratio for assigned formulas.
-Default is 3.}
-
-\item{DBEOmin}{numeric:
-DBEOmin parameter sets lower limit for DBE minus oxygen QA parameter. Default is -13.}
-
-\item{DBEOmax}{numeric:
-DBEOmax parameter sets upper limit for DBE minus oxygen QA parameter. Default is 13.}
-
-\item{Omin}{numeric:
-Omin parameter sets lower limit for oxygen number in assigned formula. Default is 0.}
-
-\item{HetCut}{character:
-HetCut turns on or off the high heteroatom QA parameter. Default is "off"}
-
-\item{NMScut}{character:
-NMScut turns on or off the nominal mass series QA parameter. Default is “on”.}
-}
-\value{
-list(Unambig = Unambig, Ambig = Ambigout, None = unassigned, MSAssign = MZ,
-         Error = Error, MSgroups = MZgroups, VK = VK)
-
-  Unambig - data frame containing unambiguous assignments
-  Ambig - data frame containing ambiguous assignments
-  None - data frame containing unassigned masses
-  MSAssign - ggplot of mass spectrum highlighting assigned/unassigned
-  Error - ggplot of the Error vs. m/z
-  MSgroups - ggplot of mass spectrum colored by molecular group
-  VK - ggplot of van Krevelen plot, colored by molecular group
-}
-\description{
-MFAssign assigns all possible molecular formulae to each
-mass in the input file, subject to user constraints on the moles of
-C, H, O, N, S, P, sodium (M), C13 (E), S34, N15, Deuterium (D), Cl, F, Cl37, NH4, and Z.
-}
-\details{
-There are user inputs for heteroatoms, adducts, and charge.
-The terms for each are Nx, Sx, Px, Ex, S34x, N15x, Dx,
-Clx, Fx, Cl37x, Mx, NH4x, and Zx. Basic QA steps are included within the
-function. More detail about these QA steps can be seen in the
-vignette and user manual attached to this package.
-Additionally, an option to remove ambiguous assignments based on choosing
-the formula with the fewest number of heteroatoms (Ohno and Ohno, 2013), and
-the CH4 vs O replacement nominal mass series (Koch et al., 2007) is included.
-Most of these QA parameters can be adjusted from outside the function.
-
-Positive mode odd-electron formula assignment is possible using the POEx
-parameter. If set to 1 positive mode odd-electron ionized masses can be
-assigned. This is only really needed for APCI and APPI ionization modes.
-This option is currently unavailable, but will be addressed in a future release.
-
-The Ox term sets the number of loops performed by the CHOFIT core by defining the
-maximum oxygen allowed to be looked for. Three oxygen is equal to one loop due to
-the low mass moiety used in CHOFIT (Perdue and Green 2015). The default setting is
-30 oxygen, so it is limited to 10 loops. It can be increased if necessary.
-
-The input dataframe should have two columns, the first column should contain the
-relative abundance or intensity for the ion mass and the second column should contain
-the ion mass, either positive or negative mode. The function can also handle an additional
-input dataframe containing the masses identified as istopic by the IsoFiltR function. The
-outputs of that function can be directly put into this function as peaks and isopeaks,
-doing so will allow likely 13C isotope masses to be match to assigned monoisotopic masses.
-The inclusion of an isotopic mass list is not required, however.
-}
-\examples{
-MFAssignAll_MSMS(peaks = Mono_df, isopeaks = Iso_df, "neg", lowMW = 200, highMW = 700)
-MFAssignALl_MSMS(peaks = Mono_df, isopeaks = Iso_df, "neg", lowMW = 100, highMW = 1000, Nx = 3, Sx = 1)
-}