From 1fdc389bf32d39528808cd1979559482b795434f Mon Sep 17 00:00:00 2001 From: skschum Date: Thu, 10 Oct 2019 18:30:39 -0400 Subject: [PATCH] Add files via upload --- MFAssignR/man/IsoFiltR.Rd | 18 +++++++++++++++++- MFAssignR/man/MFAssign.Rd | 6 +++--- MFAssignR/man/MFAssignCHO_RMD.Rd | 6 +++--- MFAssignR/man/MFAssign_RMD.Rd | 8 ++++---- MFAssignR/man/Recal.Rd | 15 ++++++++++----- 5 files changed, 37 insertions(+), 16 deletions(-) diff --git a/MFAssignR/man/IsoFiltR.Rd b/MFAssignR/man/IsoFiltR.Rd index 23fa3a4..ded67d6 100644 --- a/MFAssignR/man/IsoFiltR.Rd +++ b/MFAssignR/man/IsoFiltR.Rd @@ -4,11 +4,27 @@ \alias{IsoFiltR} \title{Identifies and separates likely isotopic masses from monoisotopic masses} \usage{ -IsoFiltR(peaks, SN = 0, Diffrat = 0.1, Sulfrat = 30) +IsoFiltR(peaks, SN = 0, Diffrat = 0.1, Sulfrat = 30, Sulferr = 5, + Carberr = 5) } \arguments{ \item{peaks}{data frame: The input 2 column data frame containing abundance and peak mass} + +\item{SN}{numeric: +Sets the noise cut for the data, peaks below this value will not be evaluated} + +\item{Diffrat}{numeric: +A value multiplied by the minimum allowed 13C ratio to expand the allowed range} + +\item{Sulfrat}{numeric: +Sets the maximum 34S ratio that is allowed for matching} + +\item{Sulferr}{numeric: +Sets the maximum allowed error (ppm) for 34S mass matching, default is 5} + +\item{Carberr}{numeric: +Sets the maximum allowed error (ppm) for 13C mass matching, default is 5} } \value{ list(Monolist, Isolist): diff --git a/MFAssignR/man/MFAssign.Rd b/MFAssignR/man/MFAssign.Rd index 54d7d0b..cd1d776 100644 --- a/MFAssignR/man/MFAssign.Rd +++ b/MFAssignR/man/MFAssign.Rd @@ -8,9 +8,9 @@ MFAssign(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, Cl37x = 0, Fx = 0, Mx = 0, NH4x = 0, Zx = 1, Sval = 2, Nval = 3, S34val = 2, N15val = 3, Pval = 5, - 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", DeNovo = 300, nLoop = 5, + Ox = 30, ppm_err = 3, iso_err = 5, 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", DeNovo = 300, nLoop = 5, SulfCheck = "on", Ambig = "off", MSMS = "off") } \arguments{ diff --git a/MFAssignR/man/MFAssignCHO_RMD.Rd b/MFAssignR/man/MFAssignCHO_RMD.Rd index ef49ac3..3eb1126 100644 --- a/MFAssignR/man/MFAssignCHO_RMD.Rd +++ b/MFAssignR/man/MFAssignCHO_RMD.Rd @@ -84,14 +84,14 @@ NMScut turns on or off the nominal mass series QA parameter. Default is “on” \item{DeNovo}{numeric: DeNovo sets the de novo cut point for the data. Default is 1000.} +\item{nLoop}{numeric: +nLoops sets the number of times the KMD and z* series assignment loops. Default is 5.} + \item{Ambig}{character: Turns on or off increased ambiguity for assignments. Default is "off".} \item{MSMS}{character: Turns on or off CH2 KMD prescreening before initial assignment. Default is "off".} - -\item{nLoops}{numeric: -nLoops sets the number of times the KMD and z* series assignment loops. Default is 5.} } \value{ list(Unambig = Unambig, Ambig = Ambigout, None = unassigned, MSAssign = MZ, diff --git a/MFAssignR/man/MFAssign_RMD.Rd b/MFAssignR/man/MFAssign_RMD.Rd index 55848a9..3404f3e 100644 --- a/MFAssignR/man/MFAssign_RMD.Rd +++ b/MFAssignR/man/MFAssign_RMD.Rd @@ -8,10 +8,10 @@ MFAssign_RMD(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, Cl37x = 0, Fx = 0, Mx = 0, NH4x = 0, Zx = 1, Sval = 2, Nval = 3, S34val = 2, - N15val = 3, Pval = 5, 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", DeNovo = 300, nLoop = 5, - SulfCheck = "on", Ambig = "off", MSMS = "off") + N15val = 3, Pval = 5, Ox = 30, ppm_err = 3, iso_err = 5, 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", DeNovo = 300, + nLoop = 5, SulfCheck = "on", Ambig = "off", MSMS = "off") } \arguments{ \item{peaks}{data frame, Monoisotopic Masses} diff --git a/MFAssignR/man/Recal.Rd b/MFAssignR/man/Recal.Rd index 50ca554..2d47720 100644 --- a/MFAssignR/man/Recal.Rd +++ b/MFAssignR/man/Recal.Rd @@ -8,8 +8,8 @@ and produces a list of the chosen recalibrants.} Recal(df, peaks, isopeaks = "none", mode, SN = 0, mzRange = 50, series1 = NA, series2 = NA, series3 = NA, series4 = NA, series5 = NA, series6 = NA, series7 = NA, series8 = NA, - series9 = NA, series10 = NA, min = 100, max = 1000, bin = 10, - obs = 2) + series9 = NA, series10 = NA, min = 100, max = 1000, bin = 14, + obs = 1, num = 5, opt = 1) } \arguments{ \item{df}{data frame output from MFAssign() or MFAssignCHO()} @@ -28,10 +28,15 @@ Recal(df, peaks, isopeaks = "none", mode, SN = 0, mzRange = 50, \item{max}{numeric - maximum mass range of the data being analyzed.} -\item{bin}{numeric - sets the mass window bins to choose recalibrants from, default is 10.} +\item{bin}{numeric - sets the mass window bins to choose recalibrants from, default is 14.} -\item{obs}{numeric - sets the number of peaks to choose as recalibrants from each bin, -default is 2} +\item{obs}{numeric - sets the number of peaks to choose as recalibrants from each bin. +Default is 1} + +\item{num}{numeric - sets the number of peaks on either side of defined recalibrant to choose +as additional recalibrants. Default is 5.} + +\item{opt}{numeric - selects the recalibration option to be used, options are 1, 2, 3, or 4} \item{series(1-10)}{character the recalibrant series, "O7_Na_4" for example, default is NA} }