From 2dcceb8f2ef25d8c793b20a5d22de7d6581e9a2a Mon Sep 17 00:00:00 2001 From: anfederico Date: Mon, 16 Oct 2023 20:08:33 -0400 Subject: [PATCH] Update packages --- DESCRIPTION | 2 +- man/gsets.Rd | 36 ++++++++++++++++++------------------ man/hyp.Rd | 24 ++++++++++++------------ man/multihyp.Rd | 24 ++++++++++++------------ man/pvector.Rd | 36 ++++++++++++++++++------------------ man/rgsets.Rd | 36 ++++++++++++++++++------------------ 6 files changed, 79 insertions(+), 79 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e3e824c..e0124d7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -12,7 +12,7 @@ Depends: R (>= 3.6.0) License: GPL-3 + file LICENSE URL: https://github.com/montilab/hypeR Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 LazyData: false Imports: ggplot2, diff --git a/man/gsets.Rd b/man/gsets.Rd index 27e2233..8a4d47b 100644 --- a/man/gsets.Rd +++ b/man/gsets.Rd @@ -37,17 +37,17 @@ print(gsets_obj) \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{gsets$new()}} -\item \href{#method-print}{\code{gsets$print()}} -\item \href{#method-list}{\code{gsets$list()}} -\item \href{#method-info}{\code{gsets$info()}} -\item \href{#method-reduce}{\code{gsets$reduce()}} -\item \href{#method-clone}{\code{gsets$clone()}} +\item \href{#method-gsets-new}{\code{gsets$new()}} +\item \href{#method-gsets-print}{\code{gsets$print()}} +\item \href{#method-gsets-list}{\code{gsets$list()}} +\item \href{#method-gsets-info}{\code{gsets$info()}} +\item \href{#method-gsets-reduce}{\code{gsets$reduce()}} +\item \href{#method-gsets-clone}{\code{gsets$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-gsets-new}{}}} \subsection{Method \code{new()}}{ Create a gsets object \subsection{Usage}{ @@ -80,8 +80,8 @@ A new gsets object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-print}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-gsets-print}{}}} \subsection{Method \code{print()}}{ Print genesets information \subsection{Usage}{ @@ -93,8 +93,8 @@ NULL } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-list}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-gsets-list}{}}} \subsection{Method \code{list()}}{ Return genesets as a list \subsection{Usage}{ @@ -106,8 +106,8 @@ A list of genesets } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-info}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-gsets-info}{}}} \subsection{Method \code{info()}}{ Returns versioning information \subsection{Usage}{ @@ -119,8 +119,8 @@ A character vector with name and version } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-reduce}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-gsets-reduce}{}}} \subsection{Method \code{reduce()}}{ Reduces genesets to a background distribution of symbols \subsection{Usage}{ @@ -139,8 +139,8 @@ A gsets object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-gsets-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/hyp.Rd b/man/hyp.Rd index 7ec2447..0a312ca 100644 --- a/man/hyp.Rd +++ b/man/hyp.Rd @@ -36,15 +36,15 @@ hyp_obj <- hyp$new(data, args=args) \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{hyp$new()}} -\item \href{#method-print}{\code{hyp$print()}} -\item \href{#method-as.data.frame}{\code{hyp$as.data.frame()}} -\item \href{#method-clone}{\code{hyp$clone()}} +\item \href{#method-hyp-new}{\code{hyp$new()}} +\item \href{#method-hyp-print}{\code{hyp$print()}} +\item \href{#method-hyp-as.data.frame}{\code{hyp$as.data.frame()}} +\item \href{#method-hyp-clone}{\code{hyp$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-hyp-new}{}}} \subsection{Method \code{new()}}{ Create a hyp object \subsection{Usage}{ @@ -69,8 +69,8 @@ A new hyp object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-print}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-hyp-print}{}}} \subsection{Method \code{print()}}{ Print hyp obect \subsection{Usage}{ @@ -82,8 +82,8 @@ NULL } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-as.data.frame}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-hyp-as.data.frame}{}}} \subsection{Method \code{as.data.frame()}}{ Extract dataframe from hyp obect \subsection{Usage}{ @@ -95,8 +95,8 @@ NULL } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-hyp-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/multihyp.Rd b/man/multihyp.Rd index 2f7fb44..0b6316e 100644 --- a/man/multihyp.Rd +++ b/man/multihyp.Rd @@ -32,15 +32,15 @@ multihyp_obj <- multihyp$new(data) \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{multihyp$new()}} -\item \href{#method-print}{\code{multihyp$print()}} -\item \href{#method-as.list}{\code{multihyp$as.list()}} -\item \href{#method-clone}{\code{multihyp$clone()}} +\item \href{#method-multihyp-new}{\code{multihyp$new()}} +\item \href{#method-multihyp-print}{\code{multihyp$print()}} +\item \href{#method-multihyp-as.list}{\code{multihyp$as.list()}} +\item \href{#method-multihyp-clone}{\code{multihyp$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-multihyp-new}{}}} \subsection{Method \code{new()}}{ Create a multihyp object \subsection{Usage}{ @@ -59,8 +59,8 @@ A new multihyp object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-print}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-multihyp-print}{}}} \subsection{Method \code{print()}}{ Print multihyp obect \subsection{Usage}{ @@ -72,8 +72,8 @@ NULL } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-as.list}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-multihyp-as.list}{}}} \subsection{Method \code{as.list()}}{ Print multihyp obect \subsection{Usage}{ @@ -85,8 +85,8 @@ A list of hyp objects as dataframes } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-multihyp-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/pvector.Rd b/man/pvector.Rd index 8f8efb4..e1c2b2e 100644 --- a/man/pvector.Rd +++ b/man/pvector.Rd @@ -19,17 +19,17 @@ A push/pop capable vector \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{pvector$new()}} -\item \href{#method-print}{\code{pvector$print()}} -\item \href{#method-length}{\code{pvector$length()}} -\item \href{#method-pop}{\code{pvector$pop()}} -\item \href{#method-push}{\code{pvector$push()}} -\item \href{#method-clone}{\code{pvector$clone()}} +\item \href{#method-pvector-new}{\code{pvector$new()}} +\item \href{#method-pvector-print}{\code{pvector$print()}} +\item \href{#method-pvector-length}{\code{pvector$length()}} +\item \href{#method-pvector-pop}{\code{pvector$pop()}} +\item \href{#method-pvector-push}{\code{pvector$push()}} +\item \href{#method-pvector-clone}{\code{pvector$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-pvector-new}{}}} \subsection{Method \code{new()}}{ Create a pvector \subsection{Usage}{ @@ -48,8 +48,8 @@ A new pvector } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-print}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-pvector-print}{}}} \subsection{Method \code{print()}}{ Print pvector \subsection{Usage}{ @@ -61,8 +61,8 @@ NULL } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-length}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-pvector-length}{}}} \subsection{Method \code{length()}}{ Get length of pvector \subsection{Usage}{ @@ -74,8 +74,8 @@ An integer } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-pop}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-pvector-pop}{}}} \subsection{Method \code{pop()}}{ Pop vector \subsection{Usage}{ @@ -87,8 +87,8 @@ Popped value } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-push}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-pvector-push}{}}} \subsection{Method \code{push()}}{ Push values \subsection{Usage}{ @@ -107,8 +107,8 @@ NULL } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-pvector-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/rgsets.Rd b/man/rgsets.Rd index 29dc71d..d010f37 100644 --- a/man/rgsets.Rd +++ b/man/rgsets.Rd @@ -32,17 +32,17 @@ A relational genesets object \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{rgsets$new()}} -\item \href{#method-print}{\code{rgsets$print()}} -\item \href{#method-info}{\code{rgsets$info()}} -\item \href{#method-reduce}{\code{rgsets$reduce()}} -\item \href{#method-subset}{\code{rgsets$subset()}} -\item \href{#method-clone}{\code{rgsets$clone()}} +\item \href{#method-rgsets-new}{\code{rgsets$new()}} +\item \href{#method-rgsets-print}{\code{rgsets$print()}} +\item \href{#method-rgsets-info}{\code{rgsets$info()}} +\item \href{#method-rgsets-reduce}{\code{rgsets$reduce()}} +\item \href{#method-rgsets-subset}{\code{rgsets$subset()}} +\item \href{#method-rgsets-clone}{\code{rgsets$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-rgsets-new}{}}} \subsection{Method \code{new()}}{ Create a rgsets object \subsection{Usage}{ @@ -78,8 +78,8 @@ A new rgsets object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-print}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-rgsets-print}{}}} \subsection{Method \code{print()}}{ Print relational genesets information \subsection{Usage}{ @@ -91,8 +91,8 @@ NULL } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-info}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-rgsets-info}{}}} \subsection{Method \code{info()}}{ Returns versioning information \subsection{Usage}{ @@ -104,8 +104,8 @@ A character vector with name and version } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-reduce}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-rgsets-reduce}{}}} \subsection{Method \code{reduce()}}{ Reduces genesets to a background distribution of symbols \subsection{Usage}{ @@ -124,8 +124,8 @@ A rgsets object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-subset}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-rgsets-subset}{}}} \subsection{Method \code{subset()}}{ Subsets genesets on a character vector of labels \subsection{Usage}{ @@ -144,8 +144,8 @@ A rgsets object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-rgsets-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{