HOGSVD: Compute HO GSVD factorization

In amalthomas111/SBF: R package to compute Shared Basis Factorization (SBF)

Compute HO GSVD factorization

Description

Function to compute HO GSVD factorization (Ponnapalli et al., 2011)

Usage

HOGSVD(
  matrix_list = NULL,
  check_col_matching = FALSE,
  col_index = NULL,
  col_sep = "_",
  verbose = FALSE
)

Arguments

matrix_list	A list containing Di matrices for joint matrix factorization. Column names of each Di matrix may or may not have information about tissue or cell type.
check_col_matching	if the column names have information about tissue/ cell type and one-to-one correspondence of tissue types across species has to be checked, set this parameter to be TRUE. Default FALSE.
col_index	If a separator separates information in column names, the col_index is the index in the column name corresponding to tissue or cell type. E.g. for column name 'hsapiens_brain', col_index is 2. Only checked if check_col_matching = TRUE. Default NULL.
col_sep	separator in column names to separate different fields. Example for column names 'hsapiens_brain', 'hsapiens_heart', etc., the separator is underscore. Set it to NULL if column matching across species has to be performed and there is no separator in the column names. Only checked if check_col_matching = TRUE. Default underscore.
verbose	if TRUE print verbose lines. Default FALSE.

Value

a list containing u, v, lambda, delta, and other outputs of HO GSVD factorization.

Examples

set.seed(1231)
mymat <- createRandomMatrices(n = 4, ncols = 3, nrows = 4:6)
hogsvd <- HOGSVD(matrix_list = mymat)
print(hogsvd$v)

amalthomas111/SBF documentation built on Sept. 2, 2022, 11:27 a.m.