Update links again

R/calculate_protein_abundance.R

@@ -22,8 +22,7 @@
 #' intensities as the protein abundance. Another option is `"iq"`, which performs protein
 #' quantification based on a maximal peptide ratio extraction algorithm that is adapted from the
 #' MaxLFQ algorithm of the MaxQuant software. Functions from the
-#' \href{https://academic.oup.com/bioinformatics/article/36/8/2611/5697917}{`iq`} package are
-#' used. Default is `"iq"`.
+#' `iq` package (\doi{10.1093/bioinformatics/btz961}) are used. Default is `"iq"`.
 #' @param for_plot a logical value indicating whether the result should be only protein intensities
 #' or protein intensities together with precursor intensities that can be used for plotting using
 #' \code{peptide_profile_plot()}. Default is \code{FALSE}.

R/data.R

@@ -33,7 +33,7 @@
 #' @format A data frame containing peptide level data from a Spectronaut report.
 #' @source Piazza, I., Beaton, N., Bruderer, R. et al. A machine learning-based chemoproteomic
 #' approach to identify drug targets and binding sites in complex proteomes. Nat Commun 11, 4200
-#' (2020). https://doi.org/10.1038/s41467-020-18071-x
+#' (2020). \doi{10.1038/s41467-020-18071-x}
 "rapamycin_10uM"
 
 #' Rapamycin dose response example data
@@ -47,13 +47,13 @@
 #' @format A data frame containing peptide level data from a Spectronaut report.
 #' @source Piazza, I., Beaton, N., Bruderer, R. et al. A machine learning-based chemoproteomic
 #' approach to identify drug targets and binding sites in complex proteomes. Nat Commun 11, 4200
-#' (2020). https://doi.org/10.1038/s41467-020-18071-x
+#' (2020). \doi{10.1038/s41467-020-18071-x}
 "rapamycin_dose_response"
 
 #' Structural analysis example data
 #'
 #' Example data used for the vignette about structural analysis. The data was obtained from
-#' \href{https://doi.org/10.1016/j.cell.2020.12.021}{Cappelletti 2021}
+#' Cappelletti et al. 2021 (\doi{10.1016/j.cell.2020.12.021})
 #' and corresponds to two separate experiments. Both experiments were limited proteolyis coupled to
 #' mass spectrometry (LiP-MS) experiments conducted on purified proteins. The first protein is
 #' phosphoglycerate kinase 1 (pgk) and it was treated with 25mM 3-phosphoglyceric acid (3PG).
@@ -69,7 +69,7 @@
 #' @source Cappelletti V, Hauser T, Piazza I, Pepelnjak M, Malinovska L, Fuhrer T, Li Y, Dörig C,
 #' Boersema P, Gillet L, Grossbach J, Dugourd A, Saez-Rodriguez J, Beyer A, Zamboni N, Caflisch A,
 #' de Souza N, Picotti P. Dynamic 3D proteomes reveal protein functional alterations at high
-#' resolution in situ. Cell. 2021 Jan 21;184(2):545-559.e22. doi: 10.1016/j.cell.2020.12.021.
+#' resolution in situ. Cell. 2021 Jan 21;184(2):545-559.e22. \doi{10.1016/j.cell.2020.12.021}.
 #' Epub 2020 Dec 23. PMID: 33357446; PMCID: PMC7836100.
 "ptsi_pgk"
 

R/fetch_eco.R

@@ -18,8 +18,7 @@
 #' essential to navigating the ever-growing (in size and complexity) corpus of scientific
 #' information."
 #'
-#' More information can be found in their
-#' \href{https://academic.oup.com/nar/article/47/D1/D1186/5165344}{publication}.
+#' More information can be found in their publication (\doi{10.1093/nar/gky1036}).
 #'
 #' @param return_relation a logical value that indicates if relational information should be returned instead
 #' the main descriptive information. This data can be used to check the relations of ECO terms to each other.