From e3a07a16919ab62fdd74efbe96aa46957e061717 Mon Sep 17 00:00:00 2001 From: jorainer Date: Mon, 19 Feb 2024 10:56:31 +0100 Subject: [PATCH] docs: fix roxygen-generated documentation --- man/MsBackend.Rd | 17 +++++++---------- man/MsBackendCached.Rd | 12 ++++++------ man/Spectra.Rd | 19 +++++++++---------- man/hidden_aliases.Rd | 22 ++++++++-------------- 4 files changed, 30 insertions(+), 40 deletions(-) diff --git a/man/MsBackend.Rd b/man/MsBackend.Rd index 634dd733..a728a05f 100644 --- a/man/MsBackend.Rd +++ b/man/MsBackend.Rd @@ -28,7 +28,6 @@ \alias{peaksVariables,MsBackend-method} \alias{centroided,MsBackend-method} \alias{centroided<-,MsBackend-method} -\alias{centroided<-,MsBackend,ANY-method} \alias{collisionEnergy,MsBackend-method} \alias{collisionEnergy<-,MsBackend-method} \alias{dataOrigin,MsBackend-method} @@ -79,7 +78,6 @@ \alias{scanIndex,MsBackend-method} \alias{selectSpectraVariables,MsBackend-method} \alias{smoothed,MsBackend-method} -\alias{smoothed<-,MsBackend,ANY-method} \alias{smoothed<-,MsBackend-method} \alias{spectraData,MsBackend-method} \alias{spectraData<-,MsBackend-method} @@ -89,11 +87,10 @@ \alias{split,MsBackend,ANY-method} \alias{supportsSetBackend,MsBackend-method} \alias{tic,MsBackend-method} -\alias{[,MsBackend,ANY,ANY,ANY-method} \alias{$,MsBackend-method} \alias{$<-,MsBackend-method} -\alias{[[,MsBackend,ANY,ANY-method} -\alias{[[<-,MsBackend,ANY,ANY,ANY-method} +\alias{[[,MsBackend-method} +\alias{[[<-,MsBackend-method} \alias{MsBackendDataFrame} \alias{backendInitialize,MsBackendDataFrame-method} \alias{MsBackendHdf5Peaks} @@ -122,7 +119,7 @@ \S4method{centroided}{MsBackend}(object) -\S4method{centroided}{MsBackend,ANY}(object) <- value +\S4method{centroided}{MsBackend}(object) <- value \S4method{collisionEnergy}{MsBackend}(object) @@ -224,7 +221,7 @@ \S4method{smoothed}{MsBackend}(object) -\S4method{smoothed}{MsBackend,ANY}(object) <- value +\S4method{smoothed}{MsBackend}(object) <- value \S4method{spectraData}{MsBackend}(object, columns = spectraVariables(object)) @@ -242,15 +239,15 @@ \S4method{tic}{MsBackend}(object, initial = TRUE) -\S4method{[}{MsBackend,ANY,ANY,ANY}(x, i, j, ..., drop = FALSE) +\S4method{[}{MsBackend}(x, i, j, ..., drop = FALSE) \S4method{$}{MsBackend}(x, name) \S4method{$}{MsBackend}(x, name) <- value -\S4method{[[}{MsBackend,ANY,ANY}(x, i, j, ...) +\S4method{[[}{MsBackend}(x, i, j, ...) -\S4method{[[}{MsBackend,ANY,ANY,ANY}(x, i, j, ...) <- value +\S4method{[[}{MsBackend}(x, i, j, ...) <- value \S4method{uniqueMsLevels}{MsBackend}(object, ...) diff --git a/man/MsBackendCached.Rd b/man/MsBackendCached.Rd index 2b13c970..c21a2758 100644 --- a/man/MsBackendCached.Rd +++ b/man/MsBackendCached.Rd @@ -9,14 +9,14 @@ \alias{spectraVariables,MsBackendCached-method} \alias{spectraData,MsBackendCached-method} \alias{spectraData<-,MsBackendCached-method} -\alias{[,MsBackendCached,ANY,ANY,ANY-method} +\alias{[,MsBackendCached-method} \alias{$,MsBackendCached-method} \alias{$<-,MsBackendCached-method} \alias{selectSpectraVariables,MsBackendCached-method} \alias{show,MsBackendCached-method} \alias{acquisitionNum,MsBackendCached-method} \alias{centroided,MsBackendCached-method} -\alias{centroided<-,MsBackendCached,ANY-method} +\alias{centroided<-,MsBackendCached-method} \alias{collisionEnergy,MsBackendCached-method} \alias{collisionEnergy<-,MsBackendCached-method} \alias{dataOrigin,MsBackendCached-method} @@ -42,7 +42,7 @@ \alias{rtime<-,MsBackendCached-method} \alias{scanIndex,MsBackendCached-method} \alias{smoothed,MsBackendCached-method} -\alias{smoothed<-,MsBackendCached,ANY-method} +\alias{smoothed<-,MsBackendCached-method} \title{Base MsBackend class providing data caching mechanism} \usage{ MsBackendCached() @@ -65,7 +65,7 @@ MsBackendCached() \S4method{spectraData}{MsBackendCached}(object) <- value -\S4method{[}{MsBackendCached,ANY,ANY,ANY}(x, i, j, ..., drop = FALSE) +\S4method{[}{MsBackendCached}(x, i, j, ..., drop = FALSE) \S4method{$}{MsBackendCached}(x, name) @@ -79,7 +79,7 @@ MsBackendCached() \S4method{centroided}{MsBackendCached}(object) -\S4method{centroided}{MsBackendCached,ANY}(object) <- value +\S4method{centroided}{MsBackendCached}(object) <- value \S4method{collisionEnergy}{MsBackendCached}(object) @@ -131,7 +131,7 @@ MsBackendCached() \S4method{smoothed}{MsBackendCached}(object) -\S4method{smoothed}{MsBackendCached,ANY}(object) <- value +\S4method{smoothed}{MsBackendCached}(object) <- value } \arguments{ \item{object}{A \code{MsBackendCached} object.} diff --git a/man/Spectra.Rd b/man/Spectra.Rd index 405323a7..183a981e 100644 --- a/man/Spectra.Rd +++ b/man/Spectra.Rd @@ -30,7 +30,7 @@ \alias{peaksData,Spectra-method} \alias{peaksVariables,Spectra-method} \alias{centroided,Spectra-method} -\alias{centroided<-,Spectra,ANY-method} +\alias{centroided<-,Spectra-method} \alias{collisionEnergy,Spectra-method} \alias{collisionEnergy<-,Spectra-method} \alias{dataOrigin,Spectra-method} @@ -65,7 +65,7 @@ \alias{scanIndex,Spectra-method} \alias{selectSpectraVariables,Spectra-method} \alias{smoothed,Spectra-method} -\alias{smoothed<-,Spectra,ANY-method} +\alias{smoothed<-,Spectra-method} \alias{spectraData,Spectra-method} \alias{spectraData<-,Spectra-method} \alias{spectraNames,Spectra-method} @@ -74,9 +74,8 @@ \alias{tic,Spectra-method} \alias{$,Spectra-method} \alias{$<-,Spectra-method} -\alias{[[,Spectra,ANY,ANY-method} -\alias{[[<-,Spectra,ANY,ANY,ANY-method} -\alias{[,Spectra,ANY,ANY,ANY-method} +\alias{[[,Spectra-method} +\alias{[[<-,Spectra-method} \alias{filterAcquisitionNum,Spectra-method} \alias{filterEmptySpectra,Spectra-method} \alias{filterDataOrigin,Spectra-method} @@ -226,7 +225,7 @@ filterPrecursorPeaks( \S4method{centroided}{Spectra}(object) -\S4method{centroided}{Spectra,ANY}(object) <- value +\S4method{centroided}{Spectra}(object) <- value \S4method{collisionEnergy}{Spectra}(object) @@ -319,7 +318,7 @@ filterPrecursorPeaks( \S4method{smoothed}{Spectra}(object) -\S4method{smoothed}{Spectra,ANY}(object) <- value +\S4method{smoothed}{Spectra}(object) <- value \S4method{spectraData}{Spectra}(object, columns = spectraVariables(object)) @@ -337,11 +336,11 @@ filterPrecursorPeaks( \S4method{$}{Spectra}(x, name) <- value -\S4method{[[}{Spectra,ANY,ANY}(x, i, j, ...) +\S4method{[[}{Spectra}(x, i, j, ...) -\S4method{[[}{Spectra,ANY,ANY,ANY}(x, i, j, ...) <- value +\S4method{[[}{Spectra}(x, i, j, ...) <- value -\S4method{[}{Spectra,ANY,ANY,ANY}(x, i, j, ..., drop = FALSE) +\S4method{[}{Spectra}(x, i, j, ..., drop = FALSE) \S4method{filterAcquisitionNum}{Spectra}( object, diff --git a/man/hidden_aliases.Rd b/man/hidden_aliases.Rd index beafff4a..c854ed22 100644 --- a/man/hidden_aliases.Rd +++ b/man/hidden_aliases.Rd @@ -35,7 +35,6 @@ \alias{acquisitionNum,MsBackendDataFrame-method} \alias{peaksData,MsBackendDataFrame-method} \alias{centroided,MsBackendDataFrame-method} -\alias{centroided<-,MsBackendDataFrame,ANY-method} \alias{centroided<-,MsBackendDataFrame-method} \alias{collisionEnergy,MsBackendDataFrame-method} \alias{collisionEnergy<-,MsBackendDataFrame-method} @@ -71,7 +70,6 @@ \alias{scanIndex,MsBackendDataFrame-method} \alias{selectSpectraVariables,MsBackendDataFrame-method} \alias{smoothed,MsBackendDataFrame-method} -\alias{smoothed<-,MsBackendDataFrame,ANY-method} \alias{smoothed<-,MsBackendDataFrame-method} \alias{spectraData,MsBackendDataFrame-method} \alias{spectraData<-,MsBackendDataFrame-method} @@ -81,7 +79,6 @@ \alias{tic,MsBackendDataFrame-method} \alias{$,MsBackendDataFrame-method} \alias{$<-,MsBackendDataFrame-method} -\alias{[,MsBackendDataFrame,ANY,ANY,ANY-method} \alias{split,MsBackendDataFrame,ANY-method} \alias{filterAcquisitionNum,MsBackendDataFrame-method} \alias{backendInitialize,MsBackendHdf5Peaks-method} @@ -99,14 +96,12 @@ \alias{spectraData,MsBackendHdf5Peaks-method} \alias{spectraData<-,MsBackendHdf5Peaks-method} \alias{$<-,MsBackendHdf5Peaks-method} -\alias{[,MsBackendHdf5Peaks,ANY,ANY,ANY-method} \alias{[,MsBackendHdf5Peaks-method} \alias{backendMerge,MsBackendHdf5Peaks-method} \alias{show,MsBackendMemory-method} \alias{backendMerge,MsBackendMemory-method} \alias{acquisitionNum,MsBackendMemory-method} \alias{centroided,MsBackendMemory-method} -\alias{centroided<-,MsBackendMemory,ANY-method} \alias{centroided<-,MsBackendMemory-method} \alias{collisionEnergy,MsBackendMemory-method} \alias{collisionEnergy<-,MsBackendMemory-method} @@ -143,7 +138,6 @@ \alias{scanIndex,MsBackendMemory-method} \alias{selectSpectraVariables,MsBackendMemory-method} \alias{smoothed,MsBackendMemory-method} -\alias{smoothed<-,MsBackendMemory,ANY-method} \alias{smoothed<-,MsBackendMemory-method} \alias{spectraData,MsBackendMemory-method} \alias{spectraData<-,MsBackendMemory-method} @@ -154,7 +148,7 @@ \alias{tic,MsBackendMemory-method} \alias{$,MsBackendMemory-method} \alias{$<-,MsBackendMemory-method} -\alias{[,MsBackendMemory,ANY,ANY,ANY-method} +\alias{[,MsBackendMemory-method} \alias{split,MsBackendMemory,ANY-method} \alias{filterAcquisitionNum,MsBackendMemory-method} \alias{backendInitialize,MsBackendMzR-method} @@ -243,7 +237,7 @@ spectrapply(object, ...) \S4method{centroided}{MsBackendDataFrame}(object) -\S4method{centroided}{MsBackendDataFrame,ANY}(object) <- value +\S4method{centroided}{MsBackendDataFrame}(object) <- value \S4method{collisionEnergy}{MsBackendDataFrame}(object) @@ -313,7 +307,7 @@ spectrapply(object, ...) \S4method{smoothed}{MsBackendDataFrame}(object) -\S4method{smoothed}{MsBackendDataFrame,ANY}(object) <- value +\S4method{smoothed}{MsBackendDataFrame}(object) <- value \S4method{spectraData}{MsBackendDataFrame}(object, columns = spectraVariables(object)) @@ -331,7 +325,7 @@ spectrapply(object, ...) \S4method{$}{MsBackendDataFrame}(x, name) <- value -\S4method{[}{MsBackendDataFrame,ANY,ANY,ANY}(x, i, j, ..., drop = FALSE) +\S4method{[}{MsBackendDataFrame}(x, i, j, ..., drop = FALSE) \S4method{split}{MsBackendDataFrame,ANY}(x, f, drop = FALSE, ...) @@ -379,7 +373,7 @@ spectrapply(object, ...) \S4method{$}{MsBackendHdf5Peaks}(x, name) <- value -\S4method{[}{MsBackendHdf5Peaks,ANY,ANY,ANY}(x, i, j, ..., drop = FALSE) +\S4method{[}{MsBackendHdf5Peaks}(x, i, j, ..., drop = FALSE) \S4method{backendMerge}{MsBackendHdf5Peaks}(object, ...) @@ -391,7 +385,7 @@ spectrapply(object, ...) \S4method{centroided}{MsBackendMemory}(object) -\S4method{centroided}{MsBackendMemory,ANY}(object) <- value +\S4method{centroided}{MsBackendMemory}(object) <- value \S4method{collisionEnergy}{MsBackendMemory}(object) @@ -463,7 +457,7 @@ spectrapply(object, ...) \S4method{smoothed}{MsBackendMemory}(object) -\S4method{smoothed}{MsBackendMemory,ANY}(object) <- value +\S4method{smoothed}{MsBackendMemory}(object) <- value \S4method{spectraData}{MsBackendMemory}(object, columns = spectraVariables(object)) @@ -483,7 +477,7 @@ spectrapply(object, ...) \S4method{$}{MsBackendMemory}(x, name) <- value -\S4method{[}{MsBackendMemory,ANY,ANY,ANY}(x, i, j, ..., drop = FALSE) +\S4method{[}{MsBackendMemory}(x, i, j, ..., drop = FALSE) \S4method{split}{MsBackendMemory,ANY}(x, f, drop = FALSE, ...)