View source: R/RNAIntegration.R
addGeneIntegrationMatrix | R Documentation |
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.
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,
dimsToUse = 1:30,
scaleDims = NULL,
corCutOff = 0.75,
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,
genesUse = NULL,
nameCell = "predictedCell",
nameGroup = "predictedGroup",
nameScore = "predictedScore",
transferParams = list(),
threads = getArchRThreads(),
verbose = TRUE,
force = FALSE,
logFile = createLogFile("addGeneIntegrationMatrix"),
...
)
ArchRProj |
An |
useMatrix |
The name of a matrix in the |
matrixName |
The name to use for the output matrix containing scRNA-seq integration to be stored in the |
reducedDims |
The name of the |
seRNA |
A |
groupATAC |
A column name in |
groupRNA |
A column name in either |
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 |
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. |
sampleCellsRNA |
An integer describing the number of scRNA-seq cells to be used for integration. |
embeddingATAC |
A |
embeddingRNA |
A |
dimsToUse |
A vector containing the dimensions from the |
scaleDims |
A boolean value that indicates whether to z-score the reduced dimensions for each cell. This is useful for minimizing
the contribution of strong biases (dominating early PCs) and lowly abundant populations. However, this may lead to stronger sample-specific
biases since it is over-weighting latent PCs. If set to |
corCutOff |
A numeric cutoff for the correlation of each dimension to the sequencing depth. If the dimension has a
correlation to sequencing depth that is greater than the |
plotUMAP |
A boolean determining whether to plot a UMAP for each integration block. |
UMAPParams |
The list of parameters to pass to the UMAP function if "plotUMAP = TRUE". See the function |
nGenes |
The number of variable genes determined by |
useImputation |
A boolean value indicating whether to use imputation for creating the Gene Score Matrix prior to integration. |
reduction |
The Seurat reduction method to use for integrating modalities. See |
addToArrow |
A boolean value indicating whether to add the log2-normalized transcript counts from the integrated matched RNA to the Arrow files. |
scaleTo |
Each column in the integrated RNA matrix will be normalized to a column sum designated by |
genesUse |
If desired a character vector of gene names to use for integration instead of determined ones from Seurat::variableGenes. |
nameCell |
A column name to add to |
nameGroup |
A column name to add to |
nameScore |
A column name to add to |
transferParams |
Additional params to be passed to |
threads |
The number of threads to be used for parallel computing. |
verbose |
A boolean value that determines whether standard output includes verbose sections. |
force |
A boolean value indicating whether to force the matrix indicated by |
logFile |
The path to a file to be used for logging ArchR output. |
... |
Additional params to be added to |
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