Create Seurat object from a grandR object

Create Seurat object from a grandR object

Usage

as.Seurat.grandR(
  data,
  modalities = c(RNA = "total", newRNA = "new"),
  hls = NULL,
  time = NULL,
  mode = c("assay", "cells", "genes", "list")
)

Arguments

data

a grandR object

modalities

vector defining modalities to include in the Seurat object (see details)

hls

half-lives for computing previous RNA, only required for "prev" modality (see details)

time

labeling time, only required for "prev" modality (see details)

mode

how to integrate modalities into seurat object (see details)

Value

a Seurat object

Details

Modalities must be a named character vector. The only allowed elements are "total" (total counts), "new" (new counts), "old" (old counts), "prev" (estimated previous time point counts). The names of the elements are further used depending on mode.

To compute the previous time point counts, a vector of half lives and the labeling time is required. The half-lives must be given in the correct order (same as in the grandR object).

The mode parameter defines how the defined modalities are represented in the Seurat object. "assay" means that for each modality, the Seurat object will contain an assay (named according to the corresponding name in modalities). "cells" means that cells will be copied for each modality and cell names are prefixed by the corresponding name in modalities (i.e., if the grandR object has 1000 cells named c1,...,c1000, and modalities=c(RNA="total",newRNA="new"), the Seurat object will have 2000 cells named RNA.c1,...,RNA.c1000,newRNA.c1,...,newRNA.c1000). "genes" means that genes fill be copied for each modality and gene names are prefixed by the corresponding name in modalities. "list" means that instead of a single Seurat object, a list of Seurat objects is returned.