From c1789245dfad5d94ccf72f7840e9838ce19a04b9 Mon Sep 17 00:00:00 2001
From: skschum <skschum@mtu.edu>
Date: Thu, 10 Oct 2019 18:31:52 -0400
Subject: [PATCH] Delete Recal_2X.Rd

---
 MFAssignR/man/Recal_2X.Rd | 72 ---------------------------------------
 1 file changed, 72 deletions(-)
 delete mode 100644 MFAssignR/man/Recal_2X.Rd

diff --git a/MFAssignR/man/Recal_2X.Rd b/MFAssignR/man/Recal_2X.Rd
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-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RecalFunctions_2X.R
-\name{Recal_2X}
-\alias{Recal_2X}
-\title{Generates a plot to visualize recalibrant series, recalibrates two mass lists,
-and produces a list of the chosen recalibrants.}
-\usage{
-Recal_2X(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 = 14,
-  obs = 1, num = 5)
-}
-\arguments{
-\item{df}{data frame output from MFAssign() or MFAssignCHO()}
-
-\item{peaks}{data frame with two columns for recalibration, generally contains "Mono" output from IsoFiltR()}
-
-\item{isopeaks}{data frame with two columns, generally containing the "Iso" output from IsoFiltR()}
-
-\item{mode}{character "neg" or "pos" depending on the ionization mode of the data}
-
-\item{SN}{numeric value of the signal-to-noise cut point for making the plot, default is 0}
-
-\item{mzRange}{numeric value defining the mass windows used for the segmented recalibration, default is 50}
-
-\item{min}{numeric - minimum mass range of the data being analyzed.}
-
-\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 14.}
-
-\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{series(1-10)}{character the recalibrant series, "O7_Na_4" for example, default is NA}
-}
-\value{
-list(MZ, Mono, Iso, RecalOut) contains the mass spectrum (MZ), recalibrated "Mono" data frame,
- recalibrated "Iso" data frame, and the recalibrants list (RecalOut)
-}
-\description{
-Recal() takes the data frame output from MFAssign functions, the outputs of
-IsoFiltR(), and the chosen recalibrant series to generate a plot for the qualitative
-assessment of the recalibrants, recalibrate the "Mono" and "Iso" outputs from IsoFiltR,
-and prepare a data frame containing the chosen recalibrants.
-}
-\details{
-This function can handle up to 10 homologous series, though it will work with fewer.
-It is important for recalibrant masses to cover the entire mass range of interest,
-and they should be among the most abundant peaks in their region of the spectrum,
-this function helps with visualizing the recalibrants.
-
-This function also recalibrates up to two mass lists using the chosen recalibrants.
-It is best to use the "Mono" and "Iso" outputs of the IsoFiltR() function.
-
-This recalibration method uses the first step from the paper from Kozhinov et al.
-2014 (Anal. Chem.) to estimate the correction term, and uses the idea of a segmented
-or "walking" recalibration from Savory et al. 2011 (Anal. Chem) to further improve
-the recalibration.
-
-These parameters will be used to identify more potential recalibrants, and the
-tallest peaks within a user defined mass range will be used as recalibrants.
-}
-\examples{
-Recal_2X(df = Data, peaks = Mono, isopeaks = Iso, mode = "neg", SN = 500, series1 = "O4_H_2", series2 = "O4_H_8", series3 = "O6_H_8")
-
-Recal_2X(df = Data, peaks = Mono, isopeaks = Iso, mode = "pos", SN = 300, series1 = "O4_Na_2", series2 = "O4_H_8", series3 = "O6_Na_8")
-}