create: Create a loom object

In mojaveazure/loomR: An R interface for loom files

Description

Create a loom object

Usage

create(filename, data, gene.attrs = NULL, cell.attrs = NULL,
  layers = NULL, chunk.dims = "auto", chunk.size = 1000,
  do.transpose = TRUE, calc.numi = FALSE, overwrite = FALSE,
  display.progress = TRUE)

Arguments

filename	The name of the new loom file
data	The data for /matrix. If cells are rows and genes are columns, set do.transpose = FALSE; otherwise, set do.transpose = TRUE
gene.attrs	A named list of vectors with extra data for genes, each vector must be as long as the number of genes in data
cell.attrs	A named list of vectors with extra data for cells, each vector must be as long as the number of cells in data
chunk.dims	A one- or two-length integer vector of chunksizes for /matrix, defaults to 'auto' to automatically determine chunksize
chunk.size	How many rows of data should we stream to the loom file at any given time?
do.transpose	Transpose the input? Should be TRUE if data has genes as rows and cells as columns
calc.numi	Calculate number of UMIs and genes expressed per cell? Will store in 'col_attrs/nUMI' and 'col_attrs/nGene', overwriting anything passed to cel.attrs; To set a custom threshold for gene expression, pass an integer value (eg. calc.numi = 5 for a threshold of five counts per cell)
overwrite	Overwrite an already existing loom file?

Value

A connection to a loom file

See Also

loom

mojaveazure/loomR documentation built on May 29, 2019, 5:44 a.m.