From 001fd9ca0ed8557339704e3adcd1c918d409bc07 Mon Sep 17 00:00:00 2001 From: Lisa Breckels Date: Wed, 16 Oct 2024 16:44:05 +0100 Subject: [PATCH] Regenerate pRolocmarkers documentation with roxygen2 --- DESCRIPTION | 2 +- NEWS.md | 9 +- ...chinelearning-functions-tagm-mcmc-helper.R | 1 - R/pRolocmarkers.R | 60 +++++++----- man/pRolocmarkers.Rd | 91 +++++++++++++------ 5 files changed, 107 insertions(+), 56 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 36ea3014..2a231323 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -142,4 +142,4 @@ Collate: clusterdist-functions.R clusterdist-framework.R qsep.R -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 diff --git a/NEWS.md b/NEWS.md index 5e743ddc..30d1a5a4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,9 +4,12 @@ - `pRolocmarkers()` has a new `version` argument, to allow for new markers versions to be added. -- 14 new marker sets have been added to `pRolocmarkers()` under `version = 2`. -- The default `version` for `pRolocmarkers()` is now `2` rather than `1`. -- Documentation for `pRolocmarkers()` has been updated to include a description of `version = 2` markers. +- 14 new marker sets have been added to `pRolocmarkers()` under + `version = 2`. +- The default `version` for `pRolocmarkers()` is now `2` rather than + `1`. +- Documentation for `pRolocmarkers()` has been updated to include a + description of `version = 2` markers. ## Changes in version 1.45.1 diff --git a/R/machinelearning-functions-tagm-mcmc-helper.R b/R/machinelearning-functions-tagm-mcmc-helper.R index 590425de..67b48732 100644 --- a/R/machinelearning-functions-tagm-mcmc-helper.R +++ b/R/machinelearning-functions-tagm-mcmc-helper.R @@ -234,7 +234,6 @@ mcmc_thin_chains <- function(x, freq = 5) { ##' @param ... Currently ignored. ##' @return A ggplot2 object. ##' @rdname mcmc-helpers -##' @rdname mcmc-plot setMethod("plot", c("MCMCParams", "character"), function(x, y, ...) { mcmc_plot_probs(x, y, n = 1) diff --git a/R/pRolocmarkers.R b/R/pRolocmarkers.R index be7f5461..eca1d7c0 100644 --- a/R/pRolocmarkers.R +++ b/R/pRolocmarkers.R @@ -1,7 +1,6 @@ -## pRoloc markers +## pRoloc markers ## data is in inst/extdata/marker_species.rda - - +## ##' This function retrieves a list of organelle markers or, if no \code{species} ##' is provided, prints a description of available marker sets. The markers can ##' be added to and \code{MSnSet} using the \code{\link{addMarkers}} function. @@ -23,37 +22,54 @@ ##' from spatial proteomics publications. References for the source publications ##' are provided below: ##' -##' * Geladaki, A., Britovšek, N.K., Breckels, L.M., Smith, T.S., Vennard, O.L., Mulvey, C.M., Crook, O.M., Gatto, L. & Lilley, K.S. (2019) Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. Nature Communications. 10 (1). doi:10.1038/s41467-018-08191-w -##' * Christopher, J.A., Breckels, L.M., Crook, O.M., Vazquez--Chantada, M., Barratt, D. & Lilley, K.S. (2024) Global proteomics indicates subcellular-specific anti-ferroptotic responses to ionizing radiation.p.2024.09.12.611851. doi:10.1101/2024.09.12.611851 -##' * Itzhak, D.N., Tyanova, S., Cox, J. & Borner, G.H. (2016) Global, quantitative and dynamic mapping of protein subcellular localization. eLife. 5. doi:10.7554/elife.16950 -##' * Villanueva, E., Smith, T., Pizzinga, M., Elzek, M., Queiroz, R.M.L., Harvey, R.F., Breckels, L.M., Crook, O.M., Monti, M., Dezi, V., Willis, A.E. & Lilley, K.S. (2023) System-wide analysis of RNA and protein subcellular localization dynamics. Nature Methods. 1–12. doi:10.1038/s41592-023-02101-9 -##' * Christoforou, A., Mulvey, C.M., Breckels, L.M., Geladaki, A., Hurrell, T., Hayward, P.C., Naake, T., Gatto, L., Viner, R., Arias, A.M. & Lilley, K.S. (2016) A draft map of the mouse pluripotent stem cell spatial proteome. Nature Communications. 7 (1). doi:10.1038/ncomms9992 -##' * Barylyuk, K., Koreny, L., Ke, H., Butterworth, S., Crook, O.M., Lassadi, I., Gupta, V., Tromer, E., Mourier, T., Stevens, T.J., Breckels, L.M., Pain, A., Lilley, K.S. & Waller, R.F. (2020) A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions. Cell Host & Microbe. 28 (5), 752-766.e9. doi:10.1016/j.chom.2020.09.011 -##' * Moloney, N.M., Barylyuk, K., Tromer, E., Crook, O.M., Breckels, L.M., Lilley, K.S., Waller, R.F. & MacGregor, P. (2023) Mapping diversity in African trypanosomes using high resolution spatial proteomics. Nature Communications. 14 (1), 4401. doi:10.1038/s41467-023-40125-z +##' \itemize{ +##' \item Geladaki, A., Britovšek, N.K., Breckels, L.M., Smith, T.S., Vennard, O.L., +##' Mulvey, C.M., Crook, O.M., Gatto, L. & Lilley, K.S. (2019) Combining LOPIT +##' with differential ultracentrifugation for high-resolution spatial proteomics. +##' Nature Communications. 10 (1). doi:10.1038/s41467-018-08191-w +##' \item Christopher, J.A., Breckels, L.M., Crook, O.M., Vazquez--Chantada, +##' M., Barratt, D. & Lilley, K.S. (2024) Global proteomics indicates +##' subcellular-specific anti-ferroptotic responses to ionizing +##' radiation.p.2024.09.12.611851. doi:10.1101/2024.09.12.611851 +##' \item Itzhak, D.N., Tyanova, S., Cox, J. & Borner, G.H. (2016) Global, +##' quantitative and dynamic mapping of protein subcellular localization. +##' eLife. 5. doi:10.7554/elife.16950 +##' \item Villanueva, E., Smith, T., Pizzinga, M., Elzek, M., Queiroz, R.M.L., +##' Harvey, R.F., Breckels, L.M., Crook, O.M., Monti, M., Dezi, V., +##' Willis, A.E. & Lilley, K.S. (2023) System-wide analysis of RNA +##' and protein subcellular localization dynamics. Nature Methods. 1–12. +##' doi:10.1038/s41592-023-02101-9 +##' \item Christoforou, A., Mulvey, C.M., Breckels, L.M., Geladaki, A., +##' Hurrell, T., Hayward, P.C., Naake, T., Gatto, L., Viner, R., +##' Arias, A.M. & Lilley, K.S. (2016) A draft map of the mouse pluripotent +##' stem cell spatial proteome. Nature Communications. 7 (1). doi:10.1038/ncomms9992 +##' \item Barylyuk, K., Koreny, L., Ke, H., Butterworth, S., Crook, O.M., +##' Lassadi, I., Gupta, V., Tromer, E., Mourier, T., Stevens, T.J., Breckels, L.M., +##' Pain, A., Lilley, K.S. & Waller, R.F. (2020) A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions. Cell Host & Microbe. 28 (5), 752-766.e9. doi:10.1016/j.chom.2020.09.011 +##' \item Moloney, N.M., Barylyuk, K., Tromer, E., Crook, O.M., Breckels, L.M., +##' Lilley, K.S., Waller, R.F. & MacGregor, P. (2023) Mapping diversity in +##' African trypanosomes using high resolution spatial proteomics. Nature +##' Communications. 14 (1), 4401. doi:10.1038/s41467-023-40125-z +##' } ##' -##' These markers are provided as a starting point to generate reliable sets of +##' Note: These markers are provided as a starting point to generate reliable sets of ##' organelle markers but still need to be verified against any new data in the ##' light of the quantitative data and the study conditions. ##' +##' @name pRolocmarkers ##' @title Organelle markers -##' -##' @param species `character(1)` defining the species of interest. For reference -##' species markers, this is just the species e.g. \code{"hsap"}. For published -##' marker sets this is the species and author name e.g. \code{"hsap_geladaki"}. -##' -##' @param version `character(1)` defining the marker version. -##' +##' @param species \code{character(1)} defining the species of interest. For reference +##' species markers, this is just the species e.g. \code{"hsap"}. For published +##' marker sets this is the species and author name e.g. \code{"hsap_geladaki"}. +##' @param version \code{character(1)} defining the marker version. ##' @return Prints a description of the available marker lists if \code{species} ##' is missing or a named character with organelle markers. -##' ##' @author Laurent Gatto -##' ##' @seealso \code{\link{addMarkers}} to add markers to an \code{MSnSet} and ##' \code{\link{markers}} for more information about marker encoding. -##' ##' @examples ##' pRolocmarkers() -##' table(pRolocmarkers("atha")) +##' pRolocmarkers("hsap") ##' table(pRolocmarkers("hsap")) pRolocmarkers <- function(species, version = "2") { ## To add new markers: diff --git a/man/pRolocmarkers.Rd b/man/pRolocmarkers.Rd index 260a013e..dfdcbf8f 100644 --- a/man/pRolocmarkers.Rd +++ b/man/pRolocmarkers.Rd @@ -3,49 +3,82 @@ \name{pRolocmarkers} \alias{pRolocmarkers} \title{Organelle markers} -\usage{ -pRolocmarkers(species) -} \arguments{ -\item{species}{The species of interest.} +\item{species}{\code{character(1)} defining the species of interest. For reference +species markers, this is just the species e.g. \code{"hsap"}. For published +marker sets this is the species and author name e.g. \code{"hsap_geladaki"}.} + +\item{version}{\code{character(1)} defining the marker version.} } \value{ -Prints a description of the available marker lists if -\code{species} is missing or a named character with organelle -markers. +Prints a description of the available marker lists if \code{species} + is missing or a named character with organelle markers. } \description{ -This function retrieves a list of organelle markers or, if no -\code{species} is provided, prints a description of available -marker sets. The markers can be added to and \code{MSnSet} using -the \code{\link{addMarkers}} function. +This function retrieves a list of organelle markers or, if no \code{species} +is provided, prints a description of available marker sets. The markers can +be added to and \code{MSnSet} using the \code{\link{addMarkers}} function. } \details{ -The markers have been contributed by various members of the -Cambridge Centre for Proteomics, in particular Dr Dan Nightingale -for yeast, Dr Andy Christoforou and Dr Claire Mulvey for human, Dr -Arnoud Groen for Arabodopsis and Dr Claire Mulvey for mouse. In -addition, original (curated) markers from the \code{pRolocdata} -datasets have been extracted (see \code{pRolocdata} for details -and references). Curation involved verification of publicly -available subcellular localisation annotation based on the -curators knowledge of the organelles/proteins considered and -tracing the original statement in the literature. +Version 1 of the markers have been contributed by various +members of the Cambridge Centre for Proteomics, in particular Dr Dan +Nightingale for yeast, Dr Andy Christoforou and Dr Claire Mulvey for human, +Dr Arnoud Groen for Arabodopsis and Dr Claire Mulvey for mouse. In addition, +original (curated) markers from the \code{pRolocdata} datasets have been +extracted (see \code{pRolocdata} for details and references). Curation +involved verification of publicly available subcellular localisation +annotation based on the curators knowledge of the organelles/proteins +considered and tracing the original statement in the literature. + +Version 2 of the markers (current default) have been updated by Charlotte +Hutchings from the Cambridge Centre for Proteomics. Reference species +marker sets are the same as those in version 1 with minor corrections and +an updated naming system. Version 2 also contains additional marker sets +from spatial proteomics publications. References for the source publications +are provided below: + +\itemize{ +\item Geladaki, A., Britovšek, N.K., Breckels, L.M., Smith, T.S., Vennard, O.L., +Mulvey, C.M., Crook, O.M., Gatto, L. & Lilley, K.S. (2019) Combining LOPIT +with differential ultracentrifugation for high-resolution spatial proteomics. +Nature Communications. 10 (1). doi:10.1038/s41467-018-08191-w +\item Christopher, J.A., Breckels, L.M., Crook, O.M., Vazquez--Chantada, +M., Barratt, D. & Lilley, K.S. (2024) Global proteomics indicates +subcellular-specific anti-ferroptotic responses to ionizing +radiation.p.2024.09.12.611851. doi:10.1101/2024.09.12.611851 +\item Itzhak, D.N., Tyanova, S., Cox, J. & Borner, G.H. (2016) Global, +quantitative and dynamic mapping of protein subcellular localization. +eLife. 5. doi:10.7554/elife.16950 +\item Villanueva, E., Smith, T., Pizzinga, M., Elzek, M., Queiroz, R.M.L., +Harvey, R.F., Breckels, L.M., Crook, O.M., Monti, M., Dezi, V., +Willis, A.E. & Lilley, K.S. (2023) System-wide analysis of RNA +and protein subcellular localization dynamics. Nature Methods. 1–12. +doi:10.1038/s41592-023-02101-9 +\item Christoforou, A., Mulvey, C.M., Breckels, L.M., Geladaki, A., +Hurrell, T., Hayward, P.C., Naake, T., Gatto, L., Viner, R., +Arias, A.M. & Lilley, K.S. (2016) A draft map of the mouse pluripotent +stem cell spatial proteome. Nature Communications. 7 (1). doi:10.1038/ncomms9992 +\item Barylyuk, K., Koreny, L., Ke, H., Butterworth, S., Crook, O.M., +Lassadi, I., Gupta, V., Tromer, E., Mourier, T., Stevens, T.J., Breckels, L.M., +Pain, A., Lilley, K.S. & Waller, R.F. (2020) A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions. Cell Host & Microbe. 28 (5), 752-766.e9. doi:10.1016/j.chom.2020.09.011 +\item Moloney, N.M., Barylyuk, K., Tromer, E., Crook, O.M., Breckels, L.M., +Lilley, K.S., Waller, R.F. & MacGregor, P. (2023) Mapping diversity in +African trypanosomes using high resolution spatial proteomics. Nature +Communications. 14 (1), 4401. doi:10.1038/s41467-023-40125-z +} -These markers are provided as a starting point to generate -reliable sets of organelle markers but still need to be verified -against any new data in the light of the quantitative data and the -study conditions. +Note: These markers are provided as a starting point to generate reliable sets of +organelle markers but still need to be verified against any new data in the +light of the quantitative data and the study conditions. } \examples{ pRolocmarkers() -table(pRolocmarkers("atha")) +pRolocmarkers("hsap") table(pRolocmarkers("hsap")) } \seealso{ -\code{\link{addMarkers}} to add markers to an -\code{MSnSet} and \code{\link{markers}} for more information about -marker encoding. +\code{\link{addMarkers}} to add markers to an \code{MSnSet} and + \code{\link{markers}} for more information about marker encoding. } \author{ Laurent Gatto