This function lists all the conflicts between packages in the metid and other packages that you have loaded.
metid_conflicts()metid_conflicts
There are four conflicts that are deliberately ignored: intersect,
union, setequal, and setdiff from dplyr. These functions
make the base equivalents generic, so shouldn't negatively affect any
existing code.
metid_conflicts()
#> ── Conflicts ────────────────────────────────────────────── metid_conflicts() ──
#> ✖ stats4::AIC() masks stats::AIC()
#> ✖ stats4::BIC() masks stats::BIC()
#> ✖ BiocGenerics::IQR() masks stats::IQR()
#> ✖ BiocGenerics::Position() masks ggplot2::Position(), base::Position()
#> ✖ S4Vectors::aggregate() masks stats::aggregate()
#> ✖ MSnbase::all.equal() masks base::all.equal()
#> ✖ massdataset::apply() masks base::apply()
#> ✖ ProtGenerics::as.list() masks S4Vectors::as.list(), BiocGenerics::as.list(), base::as.list()
#> ✖ methods::body<-() masks base::body<-()
#> ✖ massdataset::check_mass_dataset() masks metid::check_mass_dataset()
#> ✖ stats4::coef() masks stats::coef()
#> ✖ massdataset::colMeans() masks base::colMeans()
#> ✖ massdataset::colSums() masks base::colSums()
#> ✖ MSnbase::colnames<-() masks S4Vectors::colnames<-(), BiocGenerics::colnames<-(), base::colnames<-()
#> ✖ MSnbase::combine() masks Biobase::combine(), BiocGenerics::combine(), dplyr::combine()
#> ✖ S4Vectors::complete.cases() masks stats::complete.cases()
#> ✖ stats4::confint() masks stats::confint()
#> ✖ S4Vectors::cor() masks stats::cor()
#> ✖ S4Vectors::cov() masks stats::cov()
#> ✖ BiocGenerics::density() masks stats::density()
#> ✖ S4Vectors::end() masks BiocGenerics::end(), stats::end()
#> ✖ massdataset::filter() masks dplyr::filter(), metid::filter(), stats::filter()
#> ✖ S4Vectors::findMatches() masks utils::findMatches()
#> ✖ S4Vectors::first() masks dplyr::first()
#> ✖ S4Vectors::head() masks utils::head()
#> ✖ MSnbase::image() masks BiocGenerics::image(), graphics::image()
#> ✖ S4Vectors::intersect() masks BiocGenerics::intersect(), massdataset::intersect(), base::intersect()
#> ✖ methods::kronecker() masks base::kronecker()
#> ✖ dplyr::lag() masks stats::lag()
#> ✖ stats4::logLik() masks stats::logLik()
#> ✖ BiocGenerics::mad() masks stats::mad()
#> ✖ S4Vectors::na.exclude() masks stats::na.exclude()
#> ✖ S4Vectors::na.omit() masks stats::na.omit()
#> ✖ stats4::nobs() masks stats::nobs()
#> ✖ MSnbase::plot() masks stats4::plot(), graphics::plot(), base::plot()
#> ✖ stats4::profile() masks stats::profile()
#> ✖ Rcpp::prompt() masks utils::prompt()
#> ✖ BiocGenerics::relist() masks utils::relist()
#> ✖ masstools::remove_noise() masks metid::remove_noise()
#> ✖ S4Vectors::rename() masks massdataset::rename(), dplyr::rename()
#> ✖ BiocGenerics::residuals() masks stats::residuals()
#> ✖ massdataset::rowMeans() masks base::rowMeans()
#> ✖ massdataset::rowSums() masks base::rowSums()
#> ✖ MSnbase::scale() masks base::scale()
#> ✖ S4Vectors::sd() masks BiocGenerics::sd(), stats::sd()
#> ✖ MSnbase::smooth() masks ProtGenerics::smooth(), stats::smooth()
#> ✖ MSnbase::split() masks S4Vectors::split(), base::split()
#> ✖ S4Vectors::stack() masks utils::stack()
#> ✖ S4Vectors::start() masks BiocGenerics::start(), stats::start()
#> ✖ MSnbase::t() masks S4Vectors::t(), BiocGenerics::t(), base::t()
#> ✖ S4Vectors::tail() masks utils::tail()
#> ✖ MSnbase::trimws() masks base::trimws()
#> ✖ stats4::update() masks stats::update()
#> ✖ S4Vectors::var() masks BiocGenerics::var(), stats::var()
#> ✖ stats4::vcov() masks stats::vcov()
#> ✖ BiocGenerics::weights() masks stats::weights()
#> ✖ S4Vectors::window() masks stats::window()
#> ✖ S4Vectors::xtabs() masks BiocGenerics::xtabs(), stats::xtabs()