perform.sctype: Performs sctype

In connorhknight/IBRAP: Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP)

Performs sctype

Description

Performs sctype

Usage

perform.sctype(
  object,
  assay = "RAW",
  slot = "counts",
  clust.method,
  column,
  scaled = T,
  db =
    "https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/ScTypeDB_full.xlsx",
  tissue
)

Arguments

object	IBRAP S4 class object
assay	Character. String containing indicating which assay to use
slot	Character. String defining which slot in the assay to supply to Scanorama. Default = NULL
db	Character. String indicating where to collect database from. So far we only use the standard scType reference.
tissue	Character.String which tissue to subset.

Value

cell type annotation in relation to the clusterign categories that were provided

connorhknight/IBRAP documentation built on March 9, 2023, 7:01 p.m.