Perform variable gene selection over whole dataset — Variable_Features_ALL

Performs variable gene selection for LIGER object across the entire object instead of by dataset and then taking union.

Variable_Features_ALL_LIGER(
  liger_object,
  num_genes = NULL,
  var.thresh = 0.3,
  alpha.thresh = 0.99,
  tol = 1e-04,
  do.plot = FALSE,
  pt.size = 1.5,
  chunk = 1000
)

Arguments

liger_object: LIGER object name.
num_genes: Number of genes to find. Optimizes the value of var.thresh to get this number of genes, (Default is NULL).
var.thresh: Variance threshold. Main threshold used to identify variable genes. Genes with expression variance greater than threshold (relative to mean) are selected. (higher threshold -> fewer selected genes).
alpha.thresh: Alpha threshold. Controls upper bound for expected mean gene expression (lower threshold -> higher upper bound). (default 0.99)
tol: Tolerance to use for optimization if num.genes values passed in (default 0.0001). Only applicable for rliger < 2.0.0.
do.plot: Display log plot of gene variance vs. gene expression. Selected genes are plotted in green. (Default FALSE)
pt.size: Point size for plot.
chunk: size of chunks in hdf5 file. (Default 1000)

Value

A LIGER Object with variable genes in correct slot.

References

Matching function parameter text descriptions are taken from rliger::selectGenes which is called by this function after creating new temporary object/dataset. https://github.com/welch-lab/liger. (License: GPL-3).

Examples

if (FALSE) {
liger_obj <- Variable_Features_ALL_LIGER(liger_object = liger_obj, num_genes = 2000)
}