build_loom: build_loom

In aertslab/SCopeLoomR: Build .loom files (compatible with SCope) and extract data from .loom files.

build_loom

Description

Write the data given as arguments to the given file.name .loom file.

Usage

build_loom(
  file.name,
  dgem,
  title = NULL,
  genome = NULL,
  default.embedding = NULL,
  default.embedding.name = NULL,
  hierarchy = NULL,
  fbgn.gn.mapping.file.path = NULL,
  chunk.size = 1000,
  display.progress = T,
  loom.spec.version = 3
)

Arguments

file.name	A string naming the .loom file to be generated.
dgem	A matrix of the gene expression with M genes as rows and N cells as columns.
title	A short description of content of loom.
genome	The genome used for the mapping.
default.embedding	A M-by-2 data.frame of the embedding (X and Y coordinates) of the cells.
default.embedding.name	A description name for the given default.embedding
hierarchy	A named list of the 3 hierarchy levels that can be used to group looms in SCope. Use create_hierarchy().
fbgn.gn.mapping.file.path	A N-by-2 data.frame containing the mapping between the Flybase gene and the gene symbol.
chunk.size	The size of chunk of the gene expression matrix.
display.progress	Display progress when adding the gene expression matrix.

aertslab/SCopeLoomR documentation built on April 19, 2022, 11:25 a.m.