BBKNN(Batch-balancing kNN) adjustment of SVD factors

BBKNN(Batch-balancing kNN) adjustment of SVD factors

rcpp_mmutil_bbknn(
  r_svd_v,
  r_svd_u = NULL,
  r_svd_d = NULL,
  r_batches = NULL,
  knn = 10L,
  RECIPROCAL_MATCH = TRUE,
  KNN_BILINK = 10L,
  KNN_NNLIST = 10L,
  NUM_THREADS = 1L,
  USE_SINGULAR_VALUES = FALSE
)

Arguments

r_svd_v

(n x L) n number of data points

r_svd_u

(m x L) m number of features (default: NULL)

r_svd_d

(L x 1) singular values (default: NULL)

r_batches

batch names (n x 1)

knn

kNN parameter k

RECIPROCAL_MATCH

do reciprocal match (default: TRUE)

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

USE_SINGULAR_VALUES

Weight factors by the corresponding SVs

Value

a list of (1) factors.adjusted (2) D (3) V (4) knn

Details

Build batch-balancing kNN graph based on (V * D) or V data.