... | ... |
@@ -31,7 +31,8 @@ Imports: |
31 | 31 |
grDevices, |
32 | 32 |
methods, |
33 | 33 |
ggcyto (>= 1.11.4), |
34 |
- yaml |
|
34 |
+ yaml, |
|
35 |
+ lattice |
|
35 | 36 |
biocViews: ImmunoOncology, FlowCytometry, DataImport, DataRepresentation |
36 | 37 |
LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.3.7), cytolib(>= 1.3.3), RcppParallel |
37 | 38 |
Suggests: |
... | ... |
@@ -93,6 +93,7 @@ print.cytobankExperiment <- function(x, ...){ |
93 | 93 |
#' @rdname cytobankExperiment |
94 | 94 |
#' @method getCompensationMatrices cytobankExperiment |
95 | 95 |
#' @export |
96 |
+#' @aliases getCompensationMatrices |
|
96 | 97 |
#' @export getCompensationMatrices |
97 | 98 |
getCompensationMatrices.cytobankExperiment <- function(x){ |
98 | 99 |
comps <- x[["experiment"]][["compensations"]] |
... | ... |
@@ -152,6 +153,7 @@ get_panel_per_file <- function(ce){ |
152 | 153 |
#' @export |
153 | 154 |
#' @method getTransformations cytobankExperiment |
154 | 155 |
#' @export getTransformations |
156 |
+#' @aliases getTransformations |
|
155 | 157 |
getTransformations.cytobankExperiment <- function(x, ...){ |
156 | 158 |
chnls <- colnames(x) |
157 | 159 |
low.chnls <- tolower(chnls) |
... | ... |
@@ -4,8 +4,7 @@ |
4 | 4 |
\alias{compare.counts} |
5 | 5 |
\title{compare the counts to cytobank's exported csv so that the parsing result can be verified.} |
6 | 6 |
\usage{ |
7 |
-\method{compare}{counts}(gs, file, id.vars = c("FCS Filename", |
|
8 |
- "population"), ...) |
|
7 |
+compare.counts(gs, file, id.vars = c("FCS Filename", "population"), ...) |
|
9 | 8 |
} |
10 | 9 |
\arguments{ |
11 | 10 |
\item{gs}{parsed GatingSet} |
... | ... |
@@ -5,9 +5,11 @@ |
5 | 5 |
\alias{cytobankExperiment} |
6 | 6 |
\alias{print.cytobankExperiment} |
7 | 7 |
\alias{getCompensationMatrices.cytobankExperiment} |
8 |
+\alias{getCompensationMatrices} |
|
8 | 9 |
\alias{markernames,cytobankExperiment-method} |
9 | 10 |
\alias{colnames,cytobankExperiment-method} |
10 | 11 |
\alias{getTransformations.cytobankExperiment} |
12 |
+\alias{getTransformations} |
|
11 | 13 |
\alias{sampleNames,cytobankExperiment-method} |
12 | 14 |
\alias{pData,cytobankExperiment-method} |
13 | 15 |
\title{Construct cytobankExperiment object from ACS file} |