diff --git a/man/adjustRtime.Rd b/man/adjustRtime.Rd index b447be3cc..7d179b525 100644 --- a/man/adjustRtime.Rd +++ b/man/adjustRtime.Rd @@ -1,7 +1,7 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/AllGenerics.R, R/XcmsExperiment.R, -% R/functions-Params.R, R/functions-XCMSnExp.R, R/methods-OnDiskMSnExp.R, -% R/methods-Params.R, R/methods-XCMSnExp.R +% R/do_adjustRtime-functions.R, R/functions-Params.R, R/functions-XCMSnExp.R, +% R/methods-OnDiskMSnExp.R, R/methods-Params.R, R/methods-XCMSnExp.R \name{adjustRtime} \alias{adjustRtime} \alias{ObiwarpParam-class} @@ -10,6 +10,7 @@ \alias{adjustRtime,MsExperiment,ObiwarpParam-method} \alias{adjustRtime,MsExperiment,PeakGroupsParam-method} \alias{adjustRtime,XcmsExperiment,LamaParama-method} +\alias{matchLamasChromPeaks} \alias{PeakGroupsParam} \alias{LamaParama} \alias{ObiwarpParam} @@ -99,6 +100,8 @@ adjustRtime(object, param, ...) \S4method{adjustRtime}{XcmsExperiment,LamaParama}(object, param, BPPARAM = bpparam(), ...) +matchLamasChromPeaks(object, param, BPPARAM = bpparam()) + PeakGroupsParam( minFraction = 0.9, extraPeaks = 1, @@ -226,11 +229,10 @@ adjustRtimePeakGroups(object, param = PeakGroupsParam(), msLevel = 1L) \S4method{adjustRtime}{XCMSnExp,ObiwarpParam}(object, param, msLevel = 1L) } \arguments{ -\item{object}{For \code{adjustRtime}: an \code{\link[=OnDiskMSnExp]{OnDiskMSnExp()}}, \code{\link[=XCMSnExp]{XCMSnExp()}}, -\code{\link[=MsExperiment]{MsExperiment()}} or \code{\link[=XcmsExperiment]{XcmsExperiment()}} object.} +\item{object}{An object of class `XcmsExperiment` with defined ChromPeaks.} -\item{param}{The parameter object defining the alignment method (and its -setting).} +\item{param}{An object of class `LamaParama` that will later be used for +adjustment using the [adjustRtime()] function.} \item{...}{ignored.} @@ -398,6 +400,9 @@ parameter object. \code{adjustRtimeGroups} returns a \code{matrix} with the retention times of \emph{marker} features in each sample (each row one feature, each row one sample). + +A list of matrices representing the 1:1 matches between Lamas +(ref) and ChromPeaks (obs). } \description{ The \code{adjustRtime} method(s) perform retention time correction (alignment) @@ -468,6 +473,14 @@ in fine-tuning how the matching chromatographic peaks are fitted to the lamas, thereby generating a model to align the overall retention time for a single file. } + +This function quickly matches each file's ChromPeaks to Lamas, allowing the +user to evaluate the matches for each file. +} +\note{ +If there are no matches, the file retention will not be adjusted when +calling [adjustRtime()] with the same `LamaParama` and `XcmsExperiment` +object. } \section{Subset-based alignment}{