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addGeneIntegrationMatrix.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/RNAIntegration.R
\name{addGeneIntegrationMatrix}
\alias{addGeneIntegrationMatrix}
\title{Add a GeneIntegrationMatrix to ArrowFiles or an ArchRProject}
\usage{
addGeneIntegrationMatrix(
ArchRProj = NULL,
useMatrix = "GeneScoreMatrix",
matrixName = "GeneIntegrationMatrix",
reducedDims = "IterativeLSI",
seRNA = NULL,
groupATAC = NULL,
groupRNA = NULL,
groupList = NULL,
sampleCellsATAC = 10000,
sampleCellsRNA = 10000,
embeddingATAC = NULL,
embeddingRNA = NULL,
plotUMAP = TRUE,
UMAPParams = list(n_neighbors = 40, min_dist = 0.4, metric = "cosine", verbose =
FALSE),
nGenes = 2000,
useImputation = TRUE,
reduction = "cca",
addToArrow = TRUE,
scaleTo = 10000,
nameCell = "predictedCell",
nameGroup = "predictedGroup",
nameScore = "predictedScore",
transferParams = list(),
threads = getArchRThreads(),
verbose = TRUE,
force = FALSE,
logFile = createLogFile("addGeneIntegrationMatrix"),
...
)
}
\arguments{
\item{ArchRProj}{An \code{ArchRProject} object.}
\item{useMatrix}{The name of a matrix in the \code{ArchRProject} containing gene scores to be used for RNA integration.}
\item{matrixName}{The name to use for the output matrix containing scRNA-seq integration to be stored in the \code{ArchRProject}.}
\item{reducedDims}{The name of the \code{reducedDims} object (i.e. "IterativeLSI") to retrieve from the designated \code{ArchRProject}.
This \code{reducedDims} will be used in weighting the transfer of data to scRNA to scATAC. See \code{Seurat::TransferData} for more info.}
\item{seRNA}{A \code{SeuratObject} or a scRNA-seq \code{SummarizedExperiment} (cell x gene) to be integrated with the scATAC-seq data.}
\item{groupATAC}{A column name in \code{cellColData} of the \code{ArchRProj} that will be used to determine the subgroupings specified in \code{groupList}.
This is used to constrain the integration to occur across biologically relevant groups.}
\item{groupRNA}{A column name in either \code{colData} (if \code{SummarizedExperiment}) or \code{metadata} (if \code{SeuratObject}) of \code{seRNA} that
will be used to determine the subgroupings specified in \code{groupList}. This is used to constrain the integration to occur across biologically relevant groups.
Additionally this groupRNA is used for the \code{nameGroup} output of this function.}
\item{groupList}{A list of cell groupings for both ATAC-seq and RNA-seq cells to be used for RNA-ATAC integration.
This is used to constrain the integration to occur across biologically relevant groups. The format of this should be a list of groups
with subgroups of ATAC and RNA specifying cells to integrate from both platforms.
For example \code{groupList} <- list(groupA = list(ATAC = cellsATAC_A, RNA = cellsRNA_A), groupB = list(ATAC = cellsATAC_B, RNA = cellsRNA_B))}
\item{sampleCellsATAC}{An integer describing the number of scATAC-seq cells to be used for integration.
This number will be evenly sampled across the total number of cells in the ArchRProject.}
\item{sampleCellsRNA}{An integer describing the number of scRNA-seq cells to be used for integration.}
\item{embeddingATAC}{A \code{data.frame} of cell embeddings such as a UMAP for scATAC-seq cells to be used for density sampling. The \code{data.frame} object
should have a row for each single cell described in \code{row.names} and 2 columns, one for each dimension of the embedding.}
\item{embeddingRNA}{A \code{data.frame} of cell embeddings such as a UMAP for scRNA-seq cells to be used for density sampling. The \code{data.frame} object
should have a row for each single cell described in \code{row.names} and 2 columns, one for each dimension of the embedding.}
\item{plotUMAP}{A boolean determining whether to plot a UMAP for each integration block.}
\item{UMAPParams}{The list of parameters to pass to the UMAP function if "plotUMAP = TRUE". See the function \code{umap} in the uwot package.}
\item{nGenes}{The number of variable genes determined by \code{Seurat::FindVariableGenes()} to use for integration.}
\item{useImputation}{A boolean value indicating whether to use imputation for creating the Gene Score Matrix prior to integration.}
\item{reduction}{The Seurat reduction method to use for integrating modalities. See \code{Seurat::FindTransferAnchors()} for possible reduction methods.}
\item{addToArrow}{A boolean value indicating whether to add the log2-normalized transcript counts from the integrated matched RNA to the Arrow files.}
\item{scaleTo}{Each column in the integrated RNA matrix will be normalized to a column sum designated by \code{scaleTo} prior to adding to Arrow files.}
\item{nameCell}{A column name to add to \code{cellColData} for the predicted scRNA-seq cell in the specified \code{ArchRProject}. This is useful for identifying which cell was closest to the scATAC-seq cell.}
\item{nameGroup}{A column name to add to \code{cellColData} for the predicted scRNA-seq group in the specified \code{ArchRProject}. See \code{groupRNA} for more details.}
\item{nameScore}{A column name to add to \code{cellColData} for the predicted scRNA-seq score in the specified \code{ArchRProject}. These scores represent
the assignment accuracy of the group in the RNA cells. Lower scores represent ambiguous predictions and higher scores represent precise predictions.}
\item{transferParams}{Additional params to be passed to \code{Seurat::TransferData}.}
\item{threads}{The number of threads to be used for parallel computing.}
\item{verbose}{A boolean value that determines whether standard output includes verbose sections.}
\item{force}{A boolean value indicating whether to force the matrix indicated by \code{matrixName} to be overwritten if it already exists in the given \code{input}.}
\item{logFile}{The path to a file to be used for logging ArchR output.}
\item{...}{Additional params to be added to \code{Seurat::FindTransferAnchors}}
}
\description{
This function, will integrate multiple subsets of scATAC cells with a scRNA experiment, compute matched scRNA profiles and
then store this in each samples ArrowFile.
}