diff --git a/DESCRIPTION b/DESCRIPTION index e8541da..89487c6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,8 +2,8 @@ Package: msPurity Type: Package Title: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics -Version: 1.27.1 -Date: 2023-08-30 +Version: 1.31.1 +Date: 2024-05-09 Authors@R: c( person(given = "Thomas N.", family = "Lawson", email = "thomas.nigel.lawson@gmail.com", role = c("aut", "cre"), @@ -61,7 +61,7 @@ Suggests: RPostgres, RMySQL VignetteBuilder: knitr -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 Roxygen: list(markdown = TRUE) biocViews: MassSpectrometry, Metabolomics, Software Collate: diff --git a/NEWS b/NEWS index 5a16fbe..8af8a75 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,6 @@ +CHANGES IN VERSION 1.30.1 / 1.31.1 ++ Update example for purityX causing build error + CHANGES IN VERSION 1.27.1 + createMSP fix - now uses the median precursor MZ and precursor RT in the MSP file diff --git a/R/purityX-constructor.R b/R/purityX-constructor.R index 9a40535..b9fa849 100644 --- a/R/purityX-constructor.R +++ b/R/purityX-constructor.R @@ -54,14 +54,12 @@ #' #' @return a purityX object containing a dataframe of predicted purity scores #' @examples -#' msPths <- list.files(system.file("extdata", "lcms", "mzML", -#' package="msPurityData"), full.names = TRUE, -#' pattern = "LCMS_") -#' xset <- xcms::xcmsSet(msPths) -#' xset <- xcms::group(xset) -#' xset <- xcms::retcor(xset) -#' xset <- xcms::group(xset) -#' ppLCMS <- purityX(xset, cores = 1, xgroups = c(1, 2)) +#' +#' msPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "LCMS_") +#' xset <- readRDS(system.file("extdata", "tests", "xcms", "ms_only_xset_OLD.rds", package="msPurity")) +#' xset@filepaths[1] <- msPths[basename(msPths)=="LCMS_1.mzML"] +#' xset@filepaths[2] <- msPths[basename(msPths)=="LCMS_2.mzML"] +#' px <- purityX(xset, singleFile = 1) #' #' @export purityX <- function(xset, purityType="purityFWHMmedian", offsets=c(0.5, 0.5), diff --git a/man/msPurity.Rd b/man/msPurity.Rd index 2c7d7ec..b158cf3 100644 --- a/man/msPurity.Rd +++ b/man/msPurity.Rd @@ -2,8 +2,31 @@ % Please edit documentation in R/msPurity.R \docType{package} \name{msPurity} +\alias{msPurity-package} \alias{msPurity} \title{\code{msPurity} package} \description{ \href{https://bioconductor.org/packages/release/bioc/html/msPurity.html}{msPurity Bioconductor} } +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/computational-metabolomics/msPurity/} + \item Report bugs at \url{https://github.com/computational-metabolomics/msPurity/issues/new} +} + +} +\author{ +\strong{Maintainer}: Thomas N. Lawson \email{thomas.nigel.lawson@gmail.com} (\href{https://orcid.org/0000-0002-5915-7980}{ORCID}) + +Other contributors: +\itemize{ + \item Ralf Weber [contributor] + \item Martin Jones [contributor] + \item Julien Saint-Vanne [contributor] + \item Andris Jankevics [contributor] + \item Mark Viant [thesis advisor] + \item Warwick Dunn [thesis advisor] +} + +} diff --git a/man/purityX.Rd b/man/purityX.Rd index 807cf08..8c2a584 100644 --- a/man/purityX.Rd +++ b/man/purityX.Rd @@ -69,13 +69,11 @@ Constructor for the purityX class. Given an XCMS object get the anticipated precursor purity of the grouped peaks } \examples{ -msPths <- list.files(system.file("extdata", "lcms", "mzML", - package="msPurityData"), full.names = TRUE, - pattern = "LCMS_") -xset <- xcms::xcmsSet(msPths) -xset <- xcms::group(xset) -xset <- xcms::retcor(xset) -xset <- xcms::group(xset) -ppLCMS <- purityX(xset, cores = 1, xgroups = c(1, 2)) + +msPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "LCMS_") +xset <- readRDS(system.file("extdata", "tests", "xcms", "ms_only_xset_OLD.rds", package="msPurity")) +xset@filepaths[1] <- msPths[basename(msPths)=="LCMS_1.mzML"] +xset@filepaths[2] <- msPths[basename(msPths)=="LCMS_2.mzML"] +px <- purityX(xset, singleFile = 1) }