...
|
...
|
@@ -94,8 +94,34 @@ setAs("SummarizedExperiment", "poplin", function(from) {
|
94
|
94
|
|
95
|
95
|
##' @importFrom S4Vectors coolcat
|
96
|
96
|
.poplin_show <- function(object) {
|
97
|
|
- callNextMethod()
|
|
97
|
+ ## callNextMethod()
|
|
98
|
+ cat("class:", class(object), "\n")
|
|
99
|
+ cat("dim:", dim(object), "\n")
|
|
100
|
+ ## metadata()
|
|
101
|
+ expt <- names(metadata(object))
|
|
102
|
+ if (is.null(expt))
|
|
103
|
+ expt <- character(length(metadata(object)))
|
|
104
|
+ coolcat("metadata(%d): %s\n", expt)
|
|
105
|
+ ## rownames()
|
|
106
|
+ rownames <- rownames(object)
|
|
107
|
+ if (!is.null(rownames)) coolcat("rownames(%d): %s\n", rownames)
|
|
108
|
+ else cat("rownames: NULL\n")
|
|
109
|
+ ## rowData`()
|
|
110
|
+ coolcat("rowData names(%d): %s\n", names(rowData(object, use.names=FALSE)))
|
|
111
|
+ ## colnames()
|
|
112
|
+ colnames <- colnames(object)
|
|
113
|
+ if (!is.null(colnames)) coolcat("colnames(%d): %s\n", colnames)
|
|
114
|
+ else cat("colnames: NULL\n")
|
|
115
|
+ ## colData()
|
|
116
|
+ coolcat("colData names(%d): %s\n", names(colData(object)))
|
|
117
|
+ ## assays() -> alias: poplin_raw()
|
|
118
|
+ nms <- assayNames(object)
|
|
119
|
+ if (is.null(nms))
|
|
120
|
+ nms <- character(length(assays(object, withDimnames=FALSE)))
|
|
121
|
+ coolcat("poplinRawData(%d): %s\n", nms)
|
|
122
|
+ ## poplin_data()
|
98
|
123
|
coolcat("poplinData names(%d): %s\n", poplin_data_names(object))
|
|
124
|
+ ## poplin_reduced()
|
99
|
125
|
coolcat("poplinReducedData names(%d): %s\n", poplin_reduced_names(object))
|
100
|
126
|
}
|
101
|
127
|
|