diff --git a/DESCRIPTION b/DESCRIPTION index bbbb1f5..0c1991d 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -54,5 +54,5 @@ Config/testthat/edition: 3 Encoding: UTF-8 LazyData: false Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 License: MIT + file LICENSE diff --git a/man/cogaps_result.Rd b/man/cogaps_result.Rd deleted file mode 100644 index 3a64709..0000000 --- a/man/cogaps_result.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\name{cogaps_result} -\alias{cogaps_result} -\title{Latent Feature Space for each pattern} -\format{ -CogapsResult object with 24228 features and 6 samples: -\describe{ -\item{featureLoadings}{Data frame of Gene for each pattern} -\item{sampleFactors}{Data frame of cell barcodes and the 5 patterns} -} -} -\value{ -A matrix of statistics for each pattern across each barcode -} -\description{ -A CoGAPS object where the major requirements for SpaceMarkers are the -matrices of genes, barcodes and patterns learned of the latent-feature space -} diff --git a/man/getBtme.Rd b/man/getBtme.Rd new file mode 100644 index 0000000..ac755ad --- /dev/null +++ b/man/getBtme.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/preprocessing.R +\name{getBtme} +\alias{getBtme} +\title{getBtme +Load features BayesTME object} +\usage{ +getBtme(path) +} +\description{ +getBtme +Load features BayesTME object +} +\keyword{internal} diff --git a/man/getCogaps.Rd b/man/getCogaps.Rd new file mode 100644 index 0000000..a2107d6 --- /dev/null +++ b/man/getCogaps.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/preprocessing.R +\name{getCogaps} +\alias{getCogaps} +\title{getCogaps +Load features CoGAPS object} +\usage{ +getCogaps(path) +} +\description{ +getCogaps +Load features CoGAPS object +} +\keyword{internal} diff --git a/man/getSeurat.Rd b/man/getSeurat.Rd new file mode 100644 index 0000000..d6843a8 --- /dev/null +++ b/man/getSeurat.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/preprocessing.R +\name{getSeurat} +\alias{getSeurat} +\title{getSeurat +Load features Seurat object} +\usage{ +getSeurat(path) +} +\description{ +getSeurat +Load features Seurat object +} +\keyword{internal} diff --git a/man/getSpatialFeatures.Rd b/man/getSpatialFeatures.Rd index ff49895..9f05375 100644 --- a/man/getSpatialFeatures.Rd +++ b/man/getSpatialFeatures.Rd @@ -5,7 +5,7 @@ \title{getSpatialFeatures Load spatial features} \usage{ -getSpatialFeatures(filePath, method = "CoGAPS", featureNames = NULL) +getSpatialFeatures(filePath, method = "CoGAPS", featureNames = ".") } \arguments{ \item{filePath}{A string path to the location of the file containing the @@ -15,9 +15,8 @@ spatial features.} features. e.g., "CoGAPS", "Seurat", or "BayesTME".} \item{featureNames}{An array of strings specifying the column names -corresponding to the feature names. If input is NULL, in the case of CoGAPS -and BayesTME, all features are selected In the case of Seurat, all metadata -columns with "_Feature" suffix are selected.} +corresponding to the feature names or a regex string. In the case of Seurat, +all metadata columns with "_Feature" suffix are selected.} } \value{ a matrix of spatial features with barcodes associated