diff --git a/DESCRIPTION b/DESCRIPTION index b943a6e..6f4b978 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: intervals -Version: 0.15.3 +Version: 0.15.4 Type: Package Title: Tools for Working with Points and Intervals Author: Richard Bourgon diff --git a/man/Intervals-class.Rd b/man/Intervals-class.Rd index 3185a2d..7cb5e9e 100644 --- a/man/Intervals-class.Rd +++ b/man/Intervals-class.Rd @@ -106,8 +106,8 @@ \item{[}{\code{ signature(x = "Intervals_full")} } \item{[<-}{\code{ signature(x = "Intervals", i = "ANY", j = "missing", value = "Intervals_virtual")} } \item{[<-}{\code{ signature(x = "Intervals_full", i = "ANY", j = "missing", value = "Intervals_virtual")} } - \item{adjust\_closure}{\code{ signature(x = "Intervals")} } - \item{adjust\_closure}{\code{ signature(x = "Intervals_full")} } + \item{adjust_closure}{\code{ signature(x = "Intervals")} } + \item{adjust_closure}{\code{ signature(x = "Intervals_full")} } \item{closed<-}{\code{ signature(x = "Intervals")} } \item{closed<-}{\code{ signature(x = "Intervals_full")} } \item{coerce}{\code{ signature(from = "Intervals", to = "Intervals_full")} } diff --git a/man/Intervals_virtual-class.Rd b/man/Intervals_virtual-class.Rd index 3b7913c..8ccba41 100644 --- a/man/Intervals_virtual-class.Rd +++ b/man/Intervals_virtual-class.Rd @@ -65,7 +65,7 @@ \section{Methods}{ \describe{ - \item{close\_intervals}{ \code{signature(x = "Intervals_virtual")} } + \item{close_intervals}{ \code{signature(x = "Intervals_virtual")} } \item{closed}{ \code{signature(x = "Intervals_virtual")} } \item{clusters}{ \code{signature(x = "Intervals_virtual")} } \item{coerce}{ \code{signature(from = "Intervals_virtual", to = "character")} } @@ -73,21 +73,21 @@ \item{expand}{ \code{signature(x = "Intervals_virtual")} } \item{head}{ \code{signature(x = "Intervals_virtual")} } \item{initialize}{ \code{signature(.Object = "Intervals_virtual")} } - \item{interval\_complement}{ \code{signature(x = "Intervals_virtual")} } - \item{interval\_difference}{ \code{signature(x = "Intervals_virtual", y = "Intervals_virtual")} } - \item{interval\_intersection}{ \code{signature(x = "Intervals_virtual")} } - \item{interval\_union}{ \code{signature(x = "Intervals_virtual")} } + \item{interval_complement}{ \code{signature(x = "Intervals_virtual")} } + \item{interval_difference}{ \code{signature(x = "Intervals_virtual", y = "Intervals_virtual")} } + \item{interval_intersection}{ \code{signature(x = "Intervals_virtual")} } + \item{interval_union}{ \code{signature(x = "Intervals_virtual")} } \item{is.na}{ \code{signature(x = "Intervals_virtual")} } - \item{open\_intervals}{ \code{signature(x = "Intervals_virtual")} } + \item{open_intervals}{ \code{signature(x = "Intervals_virtual")} } \item{reduce}{ \code{signature(x = "Intervals_virtual")} } \item{show}{ \code{signature(object = "Intervals_virtual")} } \item{t}{ \code{signature(x = "Intervals_virtual")} } \item{tail}{ \code{signature(x = "Intervals_virtual")} } \item{type}{ \code{signature(x = "Intervals_virtual")} } \item{type<-}{ \code{signature(x = "Intervals_virtual")} } - \item{which\_nearest}{ \code{signature(from = "numeric", to = "Intervals_virtual")} } - \item{which\_nearest}{ \code{signature(from = "Intervals_virtual", to = "numeric")} } - \item{which\_nearest}{ \code{signature(from = "Intervals_virtual", to = "Intervals_virtual")} } + \item{which_nearest}{ \code{signature(from = "numeric", to = "Intervals_virtual")} } + \item{which_nearest}{ \code{signature(from = "Intervals_virtual", to = "numeric")} } + \item{which_nearest}{ \code{signature(from = "Intervals_virtual", to = "Intervals_virtual")} } } } diff --git a/man/plot.Intervals.Rd b/man/plot.Intervals.Rd index 62e59e1..b816998 100644 --- a/man/plot.Intervals.Rd +++ b/man/plot.Intervals.Rd @@ -27,7 +27,6 @@ use_points = TRUE, use_names = TRUE, names_cex = 1, - text_col = NULL, ... ) @@ -85,10 +84,6 @@ TRUE}. } - \item{text_col}{ - Color of printed labels. Only relevant if \code{use_names = TRUE}. - } - \item{...}{Other arguments for \code{\link{plot.default}}.} } diff --git a/man/sgd.Rd b/man/sgd.Rd index 1649a1f..763c61c 100644 --- a/man/sgd.Rd +++ b/man/sgd.Rd @@ -9,7 +9,7 @@ \description{ This data set contains a data frame describing a subset of the chromosome feature data represented in Fall 2007 version of - \file{saccharomyces\_cerevisiae.gff}, available for download from the + \file{saccharomyces_cerevisiae.gff}, available for download from the \emph{Saccharomyces} Genome Database (\url{https://www.yeastgenome.org:443/}). }