CIA finds a shared correlation structure betwen two different datasets, enabling integrated downstream analysis
MultiModal_CIA(object, assay.1 = "RNA", assay.2 = "CITE",
features.1 = NULL, features.2 = NULL, num.axes = 20,
normalize.variance = TRUE)Seurat object
First assay for multimodal analysis. Default is RNA
Second assay for multimodal analysis. Default is CITE for CITE-Seq analysis.
Features of assay 1 to consider (default is variable genes)
Features of assay 2 to consider (default is all features, i.e. for CITE-Seq, all antibodies)
Number of principal axes to compute and store. Default is 20, but will calculate less if either assay has <20 features.
Return the normalized row scares, so each aexis contributes equally in downstream analysis (default is T)
Returns object after CIA, with results stored in dimensional reduction cia.assay1 (ie. cia.RNA) and cia.assay2. For example, results can be visualized using DimPlot(object,reduction.use="cia.RNA")