bindSeuratObj {phemd} | R Documentation

## Attach 'seurat' object to 'Phemd' object

### Description

Allows user to attach batch-normalized reference cell data from Seurat into 'Phemd' object containing raw expression data and metadata

### Usage

    bindSeuratObj(phemd_obj, seurat_obj, batch.colname = "plt")

### Arguments

`phemd_obj` | Phemd object initialized using createDataObj
`seurat_obj` | S4 'seurat' object containing batch-normalized reference cell data
`batch.colname` | Name of column in Seurat object that denotes batch ID

### Value

'Phemd' object containing with attached Seurat object

### Examples

    my_phemdObj <- createDataObj(all_expn_data, all_genes, as.character(snames_data))
    my_seuratObj <- Seurat::CreateSeuratObject(counts = t(all_expn_data[[1]]), project = "A")
    my_seuratObj <- Seurat::FindVariableFeatures(object = my_seuratObj)
    my_seuratObj <- Seurat::ScaleData(object = my_seuratObj, do.scale=FALSE, do.center=FALSE)
    my_seuratObj <- Seurat::RunPCA(object = my_seuratObj, pc.genes = colnames(all_expn_data[[1]]), do.print = FALSE)
    my_seuratObj <- Seurat::FindNeighbors(my_seuratObj, reduction = "pca", dims.use = 1:10)
    my_seuratObj <- Seurat::FindClusters(my_seuratObj, resolution = 0.6, print.output = 0, save.SNN = TRUE)
    my_phemdObj <- bindSeuratObj(my_phemdObj, my_seuratObj)

[Package phemd version 1.1.1 Index]