RunIMA {countland}

Perform integer matrix approximation on count matrix.

Description

Perform integer matrix approximation on count matrix.

Usage

RunIMA(
  C,
  features,
  u_bounds,
  l_bounds = c(0, 0),
  maxiter = 1e+06,
  stop_crit = 1e-04,
  subsample = TRUE
)

Arguments

C

countland object

features

target number of features, integer

u_bounds

upper bounds for U and V matrices, vector of length 2

l_bounds

lower bounds for U and V matrices, vector of length 2 (default=c(0,0))

maxiter

maximum number of iterations, integer (default=1000000)

stop_crit

criterion for stopping based on difference between iterations, numeric (default=0.0001)

subsample

if TRUE, use subsampled counts (default), otherwise use counts

Value

countland object with slots matrixU, matrixV, matrixLambda

Examples

gold_path <- system.file("testdata", package = "countland", mustWork = TRUE)
gold.data <- Seurat::Read10X(data.dir = gold_path)
C <- countland(gold.data)
C <- RunIMA(C,features=10,u_bounds=c(10,10),subsample=FALSE)