Create pseudo-bulk data for pairwise comparisons

Create pseudo-bulk data for pairwise comparisons

rcpp_mmutil_aggregate_pairwise(
  mtx_file,
  row_file,
  col_file,
  r_indv,
  r_V,
  r_cols = NULL,
  r_annot = NULL,
  r_annot_mat = NULL,
  r_lab_name = NULL,
  a0 = 1,
  b0 = 1,
  eps = 1e-08,
  knn_cell = 10L,
  knn_indv = 1L,
  KNN_BILINK = 10L,
  KNN_NNLIST = 10L,
  NUM_THREADS = 1L,
  IMPUTE_BY_KNN = TRUE,
  MAX_ROW_WORD = 2L,
  ROW_WORD_SEP = "_",
  MAX_COL_WORD = 100L,
  COL_WORD_SEP = "@"
)

Arguments

mtx_file

data file

row_file

row file

col_file

column file

r_indv

membership for the cells (r_cols)

r_V

SVD factors

r_cols

cell (col) names (if we want to take a subset)

r_annot

label annotation for the (r_cols)

r_annot_mat

label annotation matrix (cell x type) (default: NULL)

r_lab_name

label names (default: everything in r_annot)

a0

hyperparameter for gamma(a0, b0) (default: 1)

b0

hyperparameter for gamma(a0, b0) (default: 1)

eps

small number (default: 1e-8)

knn_cell

k-NN matching between cells

knn_indv

k-NN matching between individuals

KNN_BILINK

num. of bidirectional links (default: 10)

KNN_NNLIST

num. of nearest neighbor lists (default: 10)

NUM_THREADS

number of threads for multi-core processing

IMPUTE_BY_KNN

imputation by kNN alone (default: TRUE)

Value

a list of inference results