Browse code

upgrade to R4.0

yingxinlin authored on 02/04/2020 03:35:14
Showing 6 changed files

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@@ -1,7 +1,7 @@
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 Package: CiteFuse
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 Type: Package
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 Title: CiteFuse: multi-modal analysis of CITE-seq data
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-Version:  0.99.4
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+Version: 0.99.5
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 Authors@R: c(
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     person("Yingxin", "Lin", email = "[email protected]", role = c("aut", "cre")
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     ),
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@@ -10,7 +10,7 @@ Authors@R: c(
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 Description: The package for multi-modal analysis of CITE-seq data.
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 License: GPL-3
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 Encoding: UTF-8
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-Depends: R (>= 3.6)
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+Depends: R (>= 4.0)
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 Imports:
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     Rcpp (>= 1.0.2),
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     RcppEigen (>= 0.3.3.5.0),
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@@ -43,7 +43,7 @@ Imports:
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     grDevices,
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     rhdf5
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 LinkingTo: Rcpp, RcppEigen
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-RoxygenNote: 7.0.2
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+RoxygenNote: 7.1.0
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 Suggests: 
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     knitr,
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     rmarkdown,
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@@ -335,7 +335,7 @@ visualiseDim <- function(sce,
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     colour_by <- NULL
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-  }else if (class(colour_by) == "character" & length(colour_by) == 1) {
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+  }else if ("character" %in% is(colour_by) & length(colour_by) == 1) {
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     df_colour_by <- .get_color_by(sce, colour_by, data_from,
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                                assay_name, altExp_name,
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@@ -359,7 +359,7 @@ visualiseDim <- function(sce,
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     shape_by <- NULL
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-  }else if (class(shape_by) == "character" & length(shape_by) == 1) {
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+  }else if ("character" %in% is(shape_by) & length(shape_by) == 1) {
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     if (!shape_by %in% names(colData(sce))) {
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@@ -4,7 +4,9 @@
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 \name{CITEseq_example}
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 \alias{CITEseq_example}
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 \title{A subset of ECCITE-seq data (control)}
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-\format{An object of class \code{list} of length 3.}
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+\format{
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+An object of class \code{list} of length 3.
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+}
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 \source{
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 Gene Expression Omnibus with the accession code GSE126310.
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 }
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@@ -4,7 +4,9 @@
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 \name{lr_pair_subset}
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 \alias{lr_pair_subset}
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 \title{A subset of Ligand Receptor Pairs}
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-\format{An object of class \code{matrix} with 50 rows and 2 columns.}
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+\format{
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+An object of class \code{matrix} (inherits from \code{array}) with 50 rows and 2 columns.
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+}
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 \usage{
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 lr_pair_subset
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 }
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@@ -4,7 +4,9 @@
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 \name{sce_control_subset}
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 \alias{sce_control_subset}
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 \title{A SingleCellExperiment of ECCITE-seq data}
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-\format{An object of class \code{SingleCellExperiment} with 1508 rows and 128 columns.}
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+\format{
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+An object of class \code{SingleCellExperiment} with 1508 rows and 128 columns.
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+}
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 \source{
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 Gene Expression Omnibus with the accession code GSE126310.
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 }
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@@ -4,7 +4,9 @@
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 \name{sce_ctcl_subset}
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 \alias{sce_ctcl_subset}
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 \title{A SingleCellExperiment of ECCITE-seq data}
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-\format{An object of class \code{SingleCellExperiment} with 1450 rows and 173 columns.}
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+\format{
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+An object of class \code{SingleCellExperiment} with 1450 rows and 173 columns.
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+}
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 \source{
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 Gene Expression Omnibus with the accession code GSE126310.
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 }