createObject: createObject

In WilsonImmunologyLab/LinQView: Integrate information from both transcriptome and cell surface protein signals to better identify cell heterogeneity

Description

Create Seurat V3 object from raw data by calling Seurat CreateSeuratObject function and CreateAssayObject function

Usage

createObject(
  data = NULL,
  project = "SeuratProject",
  min.cells = 0,
  min.features = 0,
  names.field = 1,
  names.delim = "_",
  meta.data = NULL,
  min.cells.adt = 0,
  min.features.adt = 0,
  rna = NULL,
  adt = NULL,
  hto = NULL
)

Arguments

data	data of 10X cell ranger output
project	project name for current dataset
min.cells	Same as CreateSeuratObject function in Seurat. Include features detected in at least this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff.
min.features	Same as CreateSeuratObject function in Seurat. Include cells where at least this many features are detected.
names.field	Same as CreateSeuratObject function in Seurat. For the initial identity class for each cell, choose this field from the cell's name. E.g. If your cells are named as BARCODE_CLUSTER_CELLTYPE in the input matrix, set names.field to 3 to set the initial identities to CELLTYPE.
names.delim	Same as CreateSeuratObject function in Seurat. For the initial identity class for each cell, choose this delimiter from the cell's column name. E.g. If your cells are named as BARCODE-CLUSTER-CELLTYPE, set this to "-" to separate the cell name into its component parts for picking the relevant field.
meta.data	Same as CreateSeuratObject function in Seurat. Additional cell-level metadata to add to the Seurat object. Should be a data frame where the rows are cell names and the columns are additional metadata fields.
min.cells.adt	Same as CreateAssayObject function in Seurat. Include ADT features detected in at least this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff.
min.features.adt	Same as CreateAssayObject function in Seurat. Include cells where at least this many ADT features are detected.
rna	For datasets that not generated by 10X cell ranger, user can use rna, adt, and hto to create Seurat object.
adt	For datasets that not generated by 10X cell ranger, user can use rna, adt, and hto to create Seurat object.
hto	For datasets that not generated by 10X cell ranger, user can use rna, adt, and hto to create Seurat object.
assay	assay name, default is RNA

WilsonImmunologyLab/LinQView documentation built on Jan. 3, 2022, 10 p.m.