loadMoffat: Load preprocessed data from Moffat lab sciRNA-seq3 pipeline

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Load preprocessed data from Moffat lab sciRNA-seq3 pipeline

Description

Load preprocessed data from Moffat lab sciRNA-seq3 pipeline. RT barcode and plate summary is stored in misc slot of resulting seurat object.

Usage

loadMoffat(
  import_set,
  subsample_factor,
  input_organisms,
  organism_include,
  dir
)

Arguments

import_set	Character vector specifying expression matrix (import_set[1]), PCR barcodes (import_set[2]) and RC barcodes (import_set[3]). Expression matrix will be imported successfully if barcodes are omitted.
subsample_factor	Numeric [0,1]. Subsampling factor
input_organisms	All species included in input files. One of: "Hs" - Human "Mm" - Mouse c("Hs", "Mm") - both species included
organism_include	Species to include in downstream analysis. One of: "Hs" - Human "Mm" - Mouse c("Hs", "Mm") - both species included
dir	Character. folder containing import_set files

Value

list containing Seurat Object and named gene vector.

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.