Regenerate pRolocmarkers documentation with roxygen2

DESCRIPTION

@@ -142,4 +142,4 @@ Collate:
     clusterdist-functions.R
     clusterdist-framework.R
     qsep.R
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

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
 

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)

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: