View source: R/preprocessing5.R
FetchResidualSCTModel | R Documentation |
Calculate pearson residuals of features not in the scale.data This function is the secondary function under FetchResiduals
FetchResidualSCTModel(
object,
assay = "SCT",
umi.assay = "RNA",
layer = "counts",
chunk_size = 2000,
layer.cells = NULL,
SCTModel = NULL,
reference.SCT.model = NULL,
new_features = NULL,
clip.range = NULL,
replace.value = FALSE,
verbose = FALSE
)
object |
A seurat object |
assay |
Name of the assay of the seurat object generated by SCTransform. Default is "SCT" |
umi.assay |
Name of the assay of the seurat object to fetch UMIs from. Default is "RNA" |
layer |
Name of the layer under 'umi.assay' to fetch UMIs from. Default is "counts" |
chunk_size |
Number of cells to load in memory for calculating residuals |
layer.cells |
Vector of cells to calculate the residual for. Default is NULL which uses all cells in the layer |
SCTModel |
Which SCTmodel to use from the object for calculating the residual. Will be ignored if reference.SCT.model is set |
reference.SCT.model |
If a reference SCT model should be used for calculating the residuals. When set to not NULL, ignores the 'SCTModel' paramater. |
new_features |
A vector of features to calculate the residuals for |
clip.range |
Numeric of length two specifying the min and max values the Pearson residual will be clipped to. Useful if you want to change the clip.range. |
replace.value |
Whether to replace the value of residuals if it already exists |
verbose |
Whether to print messages and progress bars |
Returns a matrix containing centered pearson residuals of added features
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