From 8ce4ca8dc4bf21493027cab0e05e781c2ddfe23d Mon Sep 17 00:00:00 2001 From: huerqiang <13766876214@163.com> Date: Fri, 21 May 2021 12:39:28 +0800 Subject: [PATCH] add `dr` slot to `compareClusterResult`, `enrichRestul` and `gseaResult` --- NEWS.md | 4 +++- R/00-AllClasses.R | 12 +++++++++--- man/compareClusterResult-class.Rd | 2 ++ man/enrichResult-class.Rd | 2 ++ man/gseaResult-class.Rd | 2 ++ 5 files changed, 18 insertions(+), 4 deletions(-) diff --git a/NEWS.md b/NEWS.md index 7f67712..e500840 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ -# DOSE 3.17.1 +# DOSE 3.19.0.991 ++ add `dr` slot to `compareClusterResult`, `enrichRestul` and `gseaResult`(2021-5-21, Fri) +# DOSE 3.17 + support setting seed for fgsea method if e.g. `gseGO(seed = TRUE)` (2020-10-28, Wed) - diff --git a/R/00-AllClasses.R b/R/00-AllClasses.R index 8e49e78..7c0d580 100644 --- a/R/00-AllClasses.R +++ b/R/00-AllClasses.R @@ -16,6 +16,7 @@ ##' @slot .call function call ##' @slot termsim Similarity between term ##' @slot method method of calculating the similarity between nodes +##' @slot dr dimension reduction result ##' @exportClass compareClusterResult ##' @author Guangchuang Yu \url{https://guangchuangyu.github.io} ##' @exportClass compareClusterResult @@ -32,7 +33,8 @@ setClass("compareClusterResult", readable = "logical", .call = "call", termsim = "matrix", - method = "character" + method = "character", + dr = "list" ) ) @@ -59,6 +61,7 @@ setClass("compareClusterResult", ##' @slot readable logical flag of gene ID in symbol or not. ##' @slot termsim Similarity between term ##' @slot method method of calculating the similarity between nodes +##' @slot dr dimension reduction result ##' @exportClass enrichResult ##' @author Guangchuang Yu \url{https://guangchuangyu.github.io} ##' @seealso \code{\link{enrichDO}} @@ -78,7 +81,8 @@ setClass("enrichResult", geneSets = "list", readable = "logical", termsim = "matrix", - method = "character" + method = "character", + dr = "list" ), prototype=prototype(readable = FALSE) ) @@ -104,6 +108,7 @@ setClass("enrichResult", ##' @slot params parameters ##' @slot gene2Symbol gene ID to Symbol ##' @slot readable whether convert gene ID to symbol +##' @slot dr dimension reduction result ##' @exportClass gseaResult ##' @author Guangchuang Yu \url{https://guangchuangyu.github.io} ##' @keywords classes @@ -120,7 +125,8 @@ setClass("gseaResult", gene2Symbol = "character", readable = "logical", termsim = "matrix", - method = "character" + method = "character", + dr = "list" ) ) diff --git a/man/compareClusterResult-class.Rd b/man/compareClusterResult-class.Rd index 740a0f3..82e65c0 100644 --- a/man/compareClusterResult-class.Rd +++ b/man/compareClusterResult-class.Rd @@ -34,6 +34,8 @@ categories at specific level or GO enrichment analysis. \item{\code{termsim}}{Similarity between term} \item{\code{method}}{method of calculating the similarity between nodes} + +\item{\code{dr}}{dimension reduction result} }} \seealso{ diff --git a/man/enrichResult-class.Rd b/man/enrichResult-class.Rd index 25a9237..7ad50ff 100644 --- a/man/enrichResult-class.Rd +++ b/man/enrichResult-class.Rd @@ -41,6 +41,8 @@ This class represents the result of enrichment analysis. \item{\code{termsim}}{Similarity between term} \item{\code{method}}{method of calculating the similarity between nodes} + +\item{\code{dr}}{dimension reduction result} }} \seealso{ diff --git a/man/gseaResult-class.Rd b/man/gseaResult-class.Rd index 9ab84ff..562340a 100644 --- a/man/gseaResult-class.Rd +++ b/man/gseaResult-class.Rd @@ -34,6 +34,8 @@ This class represents the result of GSEA analysis \item{\code{gene2Symbol}}{gene ID to Symbol} \item{\code{readable}}{whether convert gene ID to symbol} + +\item{\code{dr}}{dimension reduction result} }} \author{