| ... | ... |
@@ -6,11 +6,12 @@ |
| 6 | 6 |
#' it exists. Otherwise, the \code{useAssay}
|
| 7 | 7 |
#' \link{assay} slot in \code{x} will be used if
|
| 8 | 8 |
#' \code{x} is a \linkS4class{SingleCellExperiment} object.
|
| 9 |
-#' @param x A numeric \link{matrix} of counts or a
|
|
| 10 |
-#' \linkS4class{SingleCellExperiment}
|
|
| 11 |
-#' with the matrix located in the assay slot under \code{useAssay} in
|
|
| 12 |
-#' \code{altExp(x, altExpName)}.
|
|
| 13 |
-#' Rows represent features and columns represent cells. |
|
| 9 |
+#' @param x A \linkS4class{SingleCellExperiment}
|
|
| 10 |
+#' with the matrix located in the assay slot under \code{useAssay}.
|
|
| 11 |
+#' Rows represent features and columns represent cells. Alternatively, |
|
| 12 |
+#' any matrix-like object that can be coerced to a sparse matrix of class |
|
| 13 |
+#' "dgCMatrix" can be directly used as input. The matrix will automatically be |
|
| 14 |
+#' converted to a \linkS4class{SingleCellExperiment} object.
|
|
| 14 | 15 |
#' @param useAssay A string specifying the name of the |
| 15 | 16 |
#' \link{assay} slot to use. Default "counts".
|
| 16 | 17 |
#' @param altExpName The name for the \link{altExp} slot
|
| ... | ... |
@@ -165,7 +166,7 @@ setMethod("celda_C",
|
| 165 | 166 |
#' @rdname celda_C |
| 166 | 167 |
#' @export |
| 167 | 168 |
setMethod("celda_C",
|
| 168 |
- signature(x = "matrix"), |
|
| 169 |
+ signature(x = "ANY"), |
|
| 169 | 170 |
function(x, |
| 170 | 171 |
useAssay = "counts", |
| 171 | 172 |
altExpName = "featureSubset", |
| ... | ... |
@@ -186,6 +187,9 @@ setMethod("celda_C",
|
| 186 | 187 |
logfile = NULL, |
| 187 | 188 |
verbose = TRUE) {
|
| 188 | 189 |
|
| 190 |
+ # Convert to sparse matrix |
|
| 191 |
+ x <- as(x, "dgCMatrix") |
|
| 192 |
+ |
|
| 189 | 193 |
ls <- list() |
| 190 | 194 |
ls[[useAssay]] <- x |
| 191 | 195 |
sce <- SingleCellExperiment::SingleCellExperiment(assays = ls) |
| ... | ... |
@@ -6,11 +6,12 @@ |
| 6 | 6 |
#' it exists. Otherwise, the \code{useAssay}
|
| 7 | 7 |
#' \link{assay} slot in \code{x} will be used if
|
| 8 | 8 |
#' \code{x} is a \linkS4class{SingleCellExperiment} object.
|
| 9 |
-#' @param x A numeric \link{matrix} of counts or a
|
|
| 10 |
-#' \linkS4class{SingleCellExperiment}
|
|
| 11 |
-#' with the matrix located in the \link{assay}
|
|
| 12 |
-#' slot under \code{useAssay} in \code{altExp(x, altExpName)}.
|
|
| 13 |
-#' Rows represent features and columns represent cells. |
|
| 9 |
+#' @param x A \linkS4class{SingleCellExperiment}
|
|
| 10 |
+#' with the matrix located in the assay slot under \code{useAssay}.
|
|
| 11 |
+#' Rows represent features and columns represent cells. Alternatively, |
|
| 12 |
+#' any matrix-like object that can be coerced to a sparse matrix of class |
|
| 13 |
+#' "dgCMatrix" can be directly used as input. The matrix will automatically be |
|
| 14 |
+#' converted to a \linkS4class{SingleCellExperiment} object.
|
|
| 14 | 15 |
#' @param useAssay A string specifying the name of the |
| 15 | 16 |
#' \link{assay} slot to use. Default "counts".
|
| 16 | 17 |
#' @param altExpName The name for the \link{altExp} slot
|
| ... | ... |
@@ -194,7 +195,7 @@ setMethod("celda_CG",
|
| 194 | 195 |
#' nchains = 1) |
| 195 | 196 |
#' @export |
| 196 | 197 |
setMethod("celda_CG",
|
| 197 |
- signature(x = "matrix"), |
|
| 198 |
+ signature(x = "ANY"), |
|
| 198 | 199 |
function(x, |
| 199 | 200 |
useAssay = "counts", |
| 200 | 201 |
altExpName = "featureSubset", |
| ... | ... |
@@ -220,6 +221,9 @@ setMethod("celda_CG",
|
| 220 | 221 |
logfile = NULL, |
| 221 | 222 |
verbose = TRUE) {
|
| 222 | 223 |
|
| 224 |
+ # Convert to sparse matrix |
|
| 225 |
+ x <- as(x, "dgCMatrix") |
|
| 226 |
+ |
|
| 223 | 227 |
ls <- list() |
| 224 | 228 |
ls[[useAssay]] <- x |
| 225 | 229 |
sce <- SingleCellExperiment::SingleCellExperiment(assays = ls) |
| ... | ... |
@@ -6,10 +6,12 @@ |
| 6 | 6 |
#' it exists. Otherwise, the \code{useAssay}
|
| 7 | 7 |
#' \link{assay} slot in \code{x} will be used if
|
| 8 | 8 |
#' \code{x} is a \linkS4class{SingleCellExperiment} object.
|
| 9 |
-#' @param x A numeric \link{matrix} of counts or a
|
|
| 10 |
-#' \linkS4class{SingleCellExperiment}
|
|
| 9 |
+#' @param x A \linkS4class{SingleCellExperiment}
|
|
| 11 | 10 |
#' with the matrix located in the assay slot under \code{useAssay}.
|
| 12 |
-#' Rows represent features and columns represent cells. |
|
| 11 |
+#' Rows represent features and columns represent cells. Alternatively, |
|
| 12 |
+#' any matrix-like object that can be coerced to a sparse matrix of class |
|
| 13 |
+#' "dgCMatrix" can be directly used as input. The matrix will automatically be |
|
| 14 |
+#' converted to a \linkS4class{SingleCellExperiment} object.
|
|
| 13 | 15 |
#' @param useAssay A string specifying the name of the |
| 14 | 16 |
#' \link{assay} slot to use. Default "counts".
|
| 15 | 17 |
#' @param altExpName The name for the \link{altExp} slot
|
| ... | ... |
@@ -149,7 +151,7 @@ setMethod("celda_G",
|
| 149 | 151 |
#' @rdname celda_G |
| 150 | 152 |
#' @export |
| 151 | 153 |
setMethod("celda_G",
|
| 152 |
- signature(x = "matrix"), |
|
| 154 |
+ signature(x = "ANY"), |
|
| 153 | 155 |
function(x, |
| 154 | 156 |
useAssay = "counts", |
| 155 | 157 |
altExpName = "featureSubset", |
| ... | ... |
@@ -169,6 +171,9 @@ setMethod("celda_G",
|
| 169 | 171 |
logfile = NULL, |
| 170 | 172 |
verbose = TRUE) {
|
| 171 | 173 |
|
| 174 |
+ # Convert to sparse matrix |
|
| 175 |
+ x <- as(x, "dgCMatrix") |
|
| 176 |
+ |
|
| 172 | 177 |
ls <- list() |
| 173 | 178 |
ls[[useAssay]] <- x |
| 174 | 179 |
sce <- SingleCellExperiment::SingleCellExperiment(assays = ls) |
| ... | ... |
@@ -3,7 +3,7 @@ |
| 3 | 3 |
\name{celda_C}
|
| 4 | 4 |
\alias{celda_C}
|
| 5 | 5 |
\alias{celda_C,SingleCellExperiment-method}
|
| 6 |
-\alias{celda_C,matrix-method}
|
|
| 6 |
+\alias{celda_C,ANY-method}
|
|
| 7 | 7 |
\title{Cell clustering with Celda}
|
| 8 | 8 |
\usage{
|
| 9 | 9 |
celda_C( |
| ... | ... |
@@ -50,7 +50,7 @@ celda_C( |
| 50 | 50 |
verbose = TRUE |
| 51 | 51 |
) |
| 52 | 52 |
|
| 53 |
-\S4method{celda_C}{matrix}(
|
|
| 53 |
+\S4method{celda_C}{ANY}(
|
|
| 54 | 54 |
x, |
| 55 | 55 |
useAssay = "counts", |
| 56 | 56 |
altExpName = "featureSubset", |
| ... | ... |
@@ -73,11 +73,12 @@ celda_C( |
| 73 | 73 |
) |
| 74 | 74 |
} |
| 75 | 75 |
\arguments{
|
| 76 |
-\item{x}{A numeric \link{matrix} of counts or a
|
|
| 77 |
-\linkS4class{SingleCellExperiment}
|
|
| 78 |
-with the matrix located in the assay slot under \code{useAssay} in
|
|
| 79 |
-\code{altExp(x, altExpName)}.
|
|
| 80 |
-Rows represent features and columns represent cells.} |
|
| 76 |
+\item{x}{A \linkS4class{SingleCellExperiment}
|
|
| 77 |
+with the matrix located in the assay slot under \code{useAssay}.
|
|
| 78 |
+Rows represent features and columns represent cells. Alternatively, |
|
| 79 |
+any matrix-like object that can be coerced to a sparse matrix of class |
|
| 80 |
+"dgCMatrix" can be directly used as input. The matrix will automatically be |
|
| 81 |
+converted to a \linkS4class{SingleCellExperiment} object.}
|
|
| 81 | 82 |
|
| 82 | 83 |
\item{useAssay}{A string specifying the name of the
|
| 83 | 84 |
\link{assay} slot to use. Default "counts".}
|
| ... | ... |
@@ -3,7 +3,7 @@ |
| 3 | 3 |
\name{celda_CG}
|
| 4 | 4 |
\alias{celda_CG}
|
| 5 | 5 |
\alias{celda_CG,SingleCellExperiment-method}
|
| 6 |
-\alias{celda_CG,matrix-method}
|
|
| 6 |
+\alias{celda_CG,ANY-method}
|
|
| 7 | 7 |
\title{Cell and feature clustering with Celda}
|
| 8 | 8 |
\usage{
|
| 9 | 9 |
celda_CG( |
| ... | ... |
@@ -60,7 +60,7 @@ celda_CG( |
| 60 | 60 |
verbose = TRUE |
| 61 | 61 |
) |
| 62 | 62 |
|
| 63 |
-\S4method{celda_CG}{matrix}(
|
|
| 63 |
+\S4method{celda_CG}{ANY}(
|
|
| 64 | 64 |
x, |
| 65 | 65 |
useAssay = "counts", |
| 66 | 66 |
altExpName = "featureSubset", |
| ... | ... |
@@ -88,11 +88,12 @@ celda_CG( |
| 88 | 88 |
) |
| 89 | 89 |
} |
| 90 | 90 |
\arguments{
|
| 91 |
-\item{x}{A numeric \link{matrix} of counts or a
|
|
| 92 |
-\linkS4class{SingleCellExperiment}
|
|
| 93 |
-with the matrix located in the \link{assay}
|
|
| 94 |
-slot under \code{useAssay} in \code{altExp(x, altExpName)}.
|
|
| 95 |
-Rows represent features and columns represent cells.} |
|
| 91 |
+\item{x}{A \linkS4class{SingleCellExperiment}
|
|
| 92 |
+with the matrix located in the assay slot under \code{useAssay}.
|
|
| 93 |
+Rows represent features and columns represent cells. Alternatively, |
|
| 94 |
+any matrix-like object that can be coerced to a sparse matrix of class |
|
| 95 |
+"dgCMatrix" can be directly used as input. The matrix will automatically be |
|
| 96 |
+converted to a \linkS4class{SingleCellExperiment} object.}
|
|
| 96 | 97 |
|
| 97 | 98 |
\item{useAssay}{A string specifying the name of the
|
| 98 | 99 |
\link{assay} slot to use. Default "counts".}
|
| ... | ... |
@@ -3,7 +3,7 @@ |
| 3 | 3 |
\name{celda_G}
|
| 4 | 4 |
\alias{celda_G}
|
| 5 | 5 |
\alias{celda_G,SingleCellExperiment-method}
|
| 6 |
-\alias{celda_G,matrix-method}
|
|
| 6 |
+\alias{celda_G,ANY-method}
|
|
| 7 | 7 |
\title{Feature clustering with Celda}
|
| 8 | 8 |
\usage{
|
| 9 | 9 |
celda_G( |
| ... | ... |
@@ -48,7 +48,7 @@ celda_G( |
| 48 | 48 |
verbose = TRUE |
| 49 | 49 |
) |
| 50 | 50 |
|
| 51 |
-\S4method{celda_G}{matrix}(
|
|
| 51 |
+\S4method{celda_G}{ANY}(
|
|
| 52 | 52 |
x, |
| 53 | 53 |
useAssay = "counts", |
| 54 | 54 |
altExpName = "featureSubset", |
| ... | ... |
@@ -70,10 +70,12 @@ celda_G( |
| 70 | 70 |
) |
| 71 | 71 |
} |
| 72 | 72 |
\arguments{
|
| 73 |
-\item{x}{A numeric \link{matrix} of counts or a
|
|
| 74 |
-\linkS4class{SingleCellExperiment}
|
|
| 73 |
+\item{x}{A \linkS4class{SingleCellExperiment}
|
|
| 75 | 74 |
with the matrix located in the assay slot under \code{useAssay}.
|
| 76 |
-Rows represent features and columns represent cells.} |
|
| 75 |
+Rows represent features and columns represent cells. Alternatively, |
|
| 76 |
+any matrix-like object that can be coerced to a sparse matrix of class |
|
| 77 |
+"dgCMatrix" can be directly used as input. The matrix will automatically be |
|
| 78 |
+converted to a \linkS4class{SingleCellExperiment} object.}
|
|
| 77 | 79 |
|
| 78 | 80 |
\item{useAssay}{A string specifying the name of the
|
| 79 | 81 |
\link{assay} slot to use. Default "counts".}
|
