scAlignCreateObject {scAlign} | R Documentation

## Creates scAlign object

### Description

Creates scAlign object

### Usage

    scAlignCreateObject(
      sce.objects,
      genes.use = NULL,
      labels = list(),
      pca.reduce = FALSE,
      pcs.compute = 20,
      cca.reduce = FALSE,
      ccs.compute = 15,
      cca.standardize = TRUE,
      data.use = "scale.data",
      project.name = "scAlignProject"
    )

### Arguments

`sce.objects` | List of Seurat or Matrix objects; sample x feature.
`genes.use` | Genes to use during PCA/CCA, all genes used as default.
`labels` | List of labels for each object.
`pca.reduce` | Initial step of dimensionality be performced by PCA.
`pcs.compute` | Number of PCs to retrain for alignment.
`cca.reduce` | Initial step of dimensionality be performced by CCA.
`ccs.compute` | Number of CCs to retrain for alignment.
`cca.standardize` | Standardize the data matrices before CCA.
`data.use` | Specificies which data to use from a Seurat object for dimensionality reduction.
`project.name` | Name for current scAlign project.

### Value

Initialized scAlign object

### Examples

    library(Seurat)
    library(SingleCellExperiment)

    ## Input data, 1000 genes x 100 cells
    data = matrix(sample.int(10000, 1000*100, TRUE), 1000, 100)
    rownames(data) = paste0("gene", seq_len(1000))
    colnames(data) = paste0("cell", seq_len(100))

    age    = c(rep("young",50), rep("old",50))
    labels = c(c(rep("type1",25), rep("type2",25)), c(rep("type1",25), rep("type2",25)))

    ctrl.data = data[,which(age == "young")]
    stim.data = data[,which(age == "old")]

    ctrlSCE <- SingleCellExperiment(
                  assays = list(scale.data = data[,which(age == "young")]))

    stimSCE <- SingleCellExperiment(
                  assays = list(scale.data = data[,which(age == "old")]))

    ## Build the scAlign class object and compute PCs
    scAlignHSC = scAlignCreateObject(sce.objects = list("YOUNG"=ctrlSCE,
                                                        "OLD"=stimSCE),
                                     labels = list(labels[which(age == "young")],
                                                   labels[which(age == "old")]),
                                     pca.reduce = TRUE,
                                     pcs.compute = 50,
                                     cca.reduce = TRUE,
                                     ccs.compute = 15,
                                     project.name = "scAlign_Kowalcyzk_HSC")

[Package scAlign version 1.8.0 Index]