This function takes an object of class iCellR and runs MNN alignment. It's a wrapper for scran.
run.mnn(
x = NULL,
method = "base.mean.rank",
top.rank = 500,
gene.list = "character",
data.type = "main",
k = 20,
cos.norm = TRUE,
ndist = 3,
d = 50,
approximate = FALSE,
irlba.args = list(),
subset.row = NULL,
auto.order = FALSE,
pc.input = FALSE,
compute.variances = FALSE,
assay.type = "logcounts",
get.spikes = FALSE,
BNPARAM = NULL,
BPPARAM = SerialParam()
)An object of class iCellR.
Choose from "base.mean.rank" or "gene.model", default is "base.mean.rank". If gene.model is chosen you need to provide gene.list.
A number taking the top genes ranked by base mean, default = 500.
A charactor vector of genes to be used for PCA. If "clust.method" is set to "gene.model", default = "my_model_genes.txt".
Choose from "main" and "imputed", default = "main"
An integer scalar specifying the number of nearest neighbors to consider when identifying MNNs.
A logical scalar indicating whether cosine normalization should be performed on the input data prior to calculating distances between cells.
A numeric scalar specifying the threshold beyond which neighbours are to be ignored when computing correction vectors. Each threshold is defined in terms of the number of median distances.
Number of dimentions to pass to <U+2018>multiBatchPCA<U+2019>.
Further arguments to pass to <U+2018>multiBatchPCA<U+2019>. Setting <U+2018>approximate=TRUE<U+2019> is recommended for large data sets with many cells.
Further arguments to pass to <U+2018>multiBatchPCA<U+2019>. Setting <U+2018>approximate=TRUE<U+2019> is recommended for large data sets with many cells.
See <U+2018>?"scran-gene-selection"<U+2019>.
Logical scalar indicating whether re-ordering of batches should be performed to maximize the number of MNN pairs at each step. Alternatively an integer vector containing a permutation of <U+2018>1:N<U+2019> where <U+2018>N<U+2019> is the number of batches.
Logical scalar indicating whether the values in <U+2018>...<U+2019> are already low-dimensional, e.g., the output of <U+2018>multiBatchPCA<U+2019>.
Logical scalar indicating whether the percentage of variance lost due to non-orthogonality should be computed.
A string or integer scalar specifying the assay containing the expression values, if SingleCellExperiment objects are present in <U+2018>...<U+2019>.
See <U+2018>?"scran-gene-selection"<U+2019>. Only relevant if <U+2018>...<U+2019> contains SingleCellExperiment objects.
A BiocNeighborParam object specifying the nearest neighbor algorithm. Defaults to an exact algorithm if <U+2018>NULL<U+2019>, see <U+2018>?findKNN<U+2019> for more details.
A BiocParallelParam object specifying whether the PCA and nearest-neighbor searches should be parallelized.
An object of class iCellR.