diff --git a/man/HDF5AnnData.Rd b/man/HDF5AnnData.Rd index 2dcb3140..ba099453 100644 --- a/man/HDF5AnnData.Rd +++ b/man/HDF5AnnData.Rd @@ -86,7 +86,7 @@ HDF5AnnData constructor varm = NULL, obsp = NULL, varp = NULL, - compression = NULL + compression = c("none", "gzip", "lzf") )}\if{html}{\out{}} } @@ -138,8 +138,8 @@ annotation arrays. It must be either \code{NULL} or a named list, where each element is a sparse matrix where each dimension has length \code{n_vars}.} \item{\code{compression}}{The compression algorithm to use when writing the -HDF5 file. Can be one of \code{"GZIP"}, \code{"LZF"} or \code{"NONE"}. Defaults to -\code{"NONE"}.} +HDF5 file. Can be one of \code{"none"}, \code{"gzip"} or \code{"lzf"}. Defaults to +\code{"none"}.} } \if{html}{\out{}} } diff --git a/man/to_HDF5AnnData.Rd b/man/to_HDF5AnnData.Rd index f7142f50..e14aa376 100644 --- a/man/to_HDF5AnnData.Rd +++ b/man/to_HDF5AnnData.Rd @@ -4,14 +4,16 @@ \alias{to_HDF5AnnData} \title{Convert an AnnData object to an HDF5AnnData object} \usage{ -to_HDF5AnnData(adata, file, ...) +to_HDF5AnnData(adata, file, compression = c("none", "gzip", "lzf")) } \arguments{ \item{adata}{An AnnData object to be converted to HDF5AnnData.} \item{file}{The filename (character) of the \code{.h5ad} file.} -\item{...}{Arguments passed onto the initialization of HDF5AnnData.} +\item{compression}{The compression algorithm to use when writing the +HDF5 file. Can be one of \code{"none"}, \code{"gzip"} or \code{"lzf"}. Defaults to +\code{"none"}.} } \value{ An HDF5AnnData object with the same data as the input AnnData diff --git a/man/write_h5ad.Rd b/man/write_h5ad.Rd index 2a7a6297..8ff238b4 100644 --- a/man/write_h5ad.Rd +++ b/man/write_h5ad.Rd @@ -4,7 +4,7 @@ \alias{write_h5ad} \title{Write H5AD} \usage{ -write_h5ad(object, path, ...) +write_h5ad(object, path, compression = c("none", "gzip", "lzf")) } \arguments{ \item{object}{The object to write, either a "SingleCellExperiment" or a @@ -12,7 +12,9 @@ write_h5ad(object, path, ...) \item{path}{Path of the file to write to} -\item{...}{Extra arguments will be passed to the appropriate convertor} +\item{compression}{The compression algorithm to use when writing the +HDF5 file. Can be one of \code{"none"}, \code{"gzip"} or \code{"lzf"}. Defaults to +\code{"none"}.} } \value{ \code{path} invisibly diff --git a/man/write_h5ad_dense_array.Rd b/man/write_h5ad_dense_array.Rd index 32820f57..001fa7a6 100644 --- a/man/write_h5ad_dense_array.Rd +++ b/man/write_h5ad_dense_array.Rd @@ -14,7 +14,7 @@ write_h5ad_dense_array(value, file, name, compression, version = "0.2.0") \item{name}{Name of the element within the H5AD file} \item{compression}{The compression to use when writing the element. Can be -one of \code{"NONE"}, \code{"GZIP"} or \code{"LZF"}.} +one of \code{"none"}, \code{"gzip"} or \code{"lzf"}. Defaults to \code{"none"}.} \item{version}{Encoding version of the element to write} }