rliger: readSubset – R documentation

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readSubset

Sample data for plotting

Description

This function samples raw/normalized/scaled data from on-disk HDF5 files for plotting. This function assumes that the cell barcodes are unique across all datasets.

Usage

readSubset(
  object,
  slot.use = "norm.data",
  balance = NULL,
  max.cells = 1000,
  chunk = 1000,
  datasets.use = NULL,
  genes.use = NULL,
  rand.seed = 1,
  verbose = TRUE
)

Arguments

`object`	`liger` object. Should call normalize and selectGenes before calling.
`slot.use`	Type of data for sampling (raw.data, norm.data(default), scale.data).
`balance`	Type of sampling. NULL means that max_cells are sampled from among all cells; balance="dataset" samples up to max_cells from each dataset; balance="cluster" samples up to max_cells from each cluster.
`max.cells`	Total number of cell to sample (default 5000).
`chunk`	is the max number of cells at a time to read from disk (default 1000).
`datasets.use`	uses only the specified datasets for sampling. Default is NULL (all datasets)
`genes.use`	samples from only the specified genes. Default is NULL (all genes)
`rand.seed`	for reproducibility (default 1).
`verbose`	Print progress bar/messages (TRUE by default)

Value

liger object with sample.data slot set.

Examples

## Not run: 
# Only for online liger object (based on HDF5 files)
# Example: sample a total amount of 5000 cells from norm.data for downstream analysis 
ligerex <- readSubset(ligerex, slot.use = "norm.data", max.cells = 5000)

## End(Not run)

rliger

Linked Inference of Genomic Experimental Relationships

v1.0.0

GPL-3

Authors

Joshua Welch [aut, ctb], Chao Gao [aut, ctb, cre], Jialin Liu [aut, ctb], Joshua Sodicoff [aut, ctb], Velina Kozareva [aut, ctb], Evan Macosko [aut, ctb], Paul Hoffman [ctb], Ilya Korsunsky [ctb], Robert Lee [ctb]

Initial release

2021-04-18