Create an ArchR project and run LSI dimension reduction

Source: R/convenience_general.R

Create an ArchR project and run LSI dimension reduction

createArchRProj(
  fragmentsPath,
  genome = c("hg19", "hg38", "mm9", "mm10"),
  createArrowFiles_params = list(sampleNames = "sample1", minTSS = 0, minFrags = 0,
    maxFrags = 1e+07, minFragSize = 10, maxFragSize = 2000, offsetPlus = 0, offsetMinus =
    0, TileMatParams = list(tileSize = 5000)),
  ArchRProject_params = list(outputDirectory = getwd(), copyArrows = FALSE),
  addIterativeLSI_params = list(),
  threads = ArchR::getArchRThreads(),
  force = FALSE,
  verbose = TRUE
)

Arguments

fragmentsPath

A character vector containing the paths to the input files to use to generate the ArrowFiles. These files can be in one of the following formats: (i) scATAC tabix files, (ii) fragment files, or (iii) bam files.

genome

A string indicating the default genome to be used for all ArchR functions. Currently supported values include "hg19","hg38","mm9", and "mm10". This value is stored as a global environment variable, not part of the ArchRProject. This can be overwritten on a per-function basis using the given function's geneAnnotationand genomeAnnotation parameter. For something other than one of the currently supported, see createGeneAnnnotation() and createGenomeAnnnotation()

createArrowFiles_params

list of parameters passed to `ArchR::createArrowFiles`

ArchRProject_params

list of parameters passed to `ArchR::ArchRProject`

addIterativeLSI_params

list of parameters passed to `ArchR::addIterativeLSI`

threads

number of threads to use. Default = `ArchR::getArchRThreads()`

force

Default = FALSE

verbose

Default = TRUE

Value

An ArchR project with GeneScoreMatrix, TileMatrix, and TileMatrix-based LSI