... | ... |
@@ -1,7 +1,7 @@ |
1 | 1 |
Package: CiteFuse |
2 | 2 |
Type: Package |
3 | 3 |
Title: CiteFuse: multi-modal analysis of CITE-seq data |
4 |
-Version: 0.99.4 |
|
4 |
+Version: 0.99.5 |
|
5 | 5 |
Authors@R: c( |
6 | 6 |
person("Yingxin", "Lin", email = "[email protected]", role = c("aut", "cre") |
7 | 7 |
), |
... | ... |
@@ -10,7 +10,7 @@ Authors@R: c( |
10 | 10 |
Description: The package for multi-modal analysis of CITE-seq data. |
11 | 11 |
License: GPL-3 |
12 | 12 |
Encoding: UTF-8 |
13 |
-Depends: R (>= 3.6) |
|
13 |
+Depends: R (>= 4.0) |
|
14 | 14 |
Imports: |
15 | 15 |
Rcpp (>= 1.0.2), |
16 | 16 |
RcppEigen (>= 0.3.3.5.0), |
... | ... |
@@ -43,7 +43,7 @@ Imports: |
43 | 43 |
grDevices, |
44 | 44 |
rhdf5 |
45 | 45 |
LinkingTo: Rcpp, RcppEigen |
46 |
-RoxygenNote: 7.0.2 |
|
46 |
+RoxygenNote: 7.1.0 |
|
47 | 47 |
Suggests: |
48 | 48 |
knitr, |
49 | 49 |
rmarkdown, |
... | ... |
@@ -335,7 +335,7 @@ visualiseDim <- function(sce, |
335 | 335 |
|
336 | 336 |
colour_by <- NULL |
337 | 337 |
|
338 |
- }else if (class(colour_by) == "character" & length(colour_by) == 1) { |
|
338 |
+ }else if ("character" %in% is(colour_by) & length(colour_by) == 1) { |
|
339 | 339 |
|
340 | 340 |
df_colour_by <- .get_color_by(sce, colour_by, data_from, |
341 | 341 |
assay_name, altExp_name, |
... | ... |
@@ -359,7 +359,7 @@ visualiseDim <- function(sce, |
359 | 359 |
|
360 | 360 |
shape_by <- NULL |
361 | 361 |
|
362 |
- }else if (class(shape_by) == "character" & length(shape_by) == 1) { |
|
362 |
+ }else if ("character" %in% is(shape_by) & length(shape_by) == 1) { |
|
363 | 363 |
|
364 | 364 |
if (!shape_by %in% names(colData(sce))) { |
365 | 365 |
|
... | ... |
@@ -4,7 +4,9 @@ |
4 | 4 |
\name{CITEseq_example} |
5 | 5 |
\alias{CITEseq_example} |
6 | 6 |
\title{A subset of ECCITE-seq data (control)} |
7 |
-\format{An object of class \code{list} of length 3.} |
|
7 |
+\format{ |
|
8 |
+An object of class \code{list} of length 3. |
|
9 |
+} |
|
8 | 10 |
\source{ |
9 | 11 |
Gene Expression Omnibus with the accession code GSE126310. |
10 | 12 |
} |
... | ... |
@@ -4,7 +4,9 @@ |
4 | 4 |
\name{lr_pair_subset} |
5 | 5 |
\alias{lr_pair_subset} |
6 | 6 |
\title{A subset of Ligand Receptor Pairs} |
7 |
-\format{An object of class \code{matrix} with 50 rows and 2 columns.} |
|
7 |
+\format{ |
|
8 |
+An object of class \code{matrix} (inherits from \code{array}) with 50 rows and 2 columns. |
|
9 |
+} |
|
8 | 10 |
\usage{ |
9 | 11 |
lr_pair_subset |
10 | 12 |
} |
... | ... |
@@ -4,7 +4,9 @@ |
4 | 4 |
\name{sce_control_subset} |
5 | 5 |
\alias{sce_control_subset} |
6 | 6 |
\title{A SingleCellExperiment of ECCITE-seq data} |
7 |
-\format{An object of class \code{SingleCellExperiment} with 1508 rows and 128 columns.} |
|
7 |
+\format{ |
|
8 |
+An object of class \code{SingleCellExperiment} with 1508 rows and 128 columns. |
|
9 |
+} |
|
8 | 10 |
\source{ |
9 | 11 |
Gene Expression Omnibus with the accession code GSE126310. |
10 | 12 |
} |
... | ... |
@@ -4,7 +4,9 @@ |
4 | 4 |
\name{sce_ctcl_subset} |
5 | 5 |
\alias{sce_ctcl_subset} |
6 | 6 |
\title{A SingleCellExperiment of ECCITE-seq data} |
7 |
-\format{An object of class \code{SingleCellExperiment} with 1450 rows and 173 columns.} |
|
7 |
+\format{ |
|
8 |
+An object of class \code{SingleCellExperiment} with 1450 rows and 173 columns. |
|
9 |
+} |
|
8 | 10 |
\source{ |
9 | 11 |
Gene Expression Omnibus with the accession code GSE126310. |
10 | 12 |
} |