project_data: Project data from one object into the UMAP embedding a single...

In scfurl/viewmaster: This package aims annotate scRNAseq data according to a reference

Project data from one object into the UMAP embedding a single cell object

Description

Adapted from: ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis Jeffrey M. Granja, M. Ryan Corces, Sarah E. Pierce, S. Tansu Bagdatli, Hani Choudhry, Howard Y. Chang, William J. Greenleaf doi: https://doi.org/10.1101/2020.04.28.066498

Usage

project_data(
  projector = NULL,
  projectee = NULL,
  ncells_coembedding = 5000,
  scale = F,
  reduced_dim = "LSI",
  embedding = "UMAP",
  make_pseudo_single_cells = FALSE,
  features = c("annotation-based", "range-based"),
  n = 250,
  verbose = TRUE,
  threads = 6,
  seed = 2020,
  force = F
)

Arguments

projector	cell_data_set object with a reduced dimension matrix (currently LSI supported) as specified in reduced_dim argument and a model used to create a low dimensional embedding
projectee	a SummarizedExperiment type object (cell_data_set currently supported) to be projected using the models contained in the projector
ncells_coembedding	number of cells in the projector to use in in the co-embedding with simulated single cells; default is 5000, will automatically default to the total number of cells in the projector if less than this value.
reduced_dim	A string specifying the reducedDim (currently LSI supported).
embedding	A string specifying embedding type (currently UMAP supported).
make_pseudo_single_cells	whether to make pseudo-single cells from the data in the projectee (set this to true for bulk data)
n	An integer specifying the number of subsampled "pseudo single cells" per bulk sample. Note this is only relevant if make_pseudo_single_cells is TRUE
verbose	A boolean value indicating whether to use verbose output during execution of this function. Can be set to FALSE for a cleaner output.
threads	The number of threads used for parallel execution

scfurl/viewmaster documentation built on Nov. 22, 2022, 2:59 p.m.