Create data matrix for NMF — create_data • JACUSA2helper

Create data matrix from JACUSA2 output object for non-negative matrix factorization.

Usage

create_data(
  result,
  scores = c("score", "deletion_score", "insertion_score"),
  ref_context = "A",
  context = 2,
  rename_score = "call2_score",
  meta_cond = TRUE
)

Arguments

result: JACUSA2 result object.
scores: Vector of strings. Columns in JACUSA2 result object to use as scores. Default: "score", "insertion_score", "deletion_score"
ref_context: reference context of a potential site. Default: "A".
context: number of nucleotides to consider around a potential site. Default: 2.
rename_score: Rename column "score". Default: "call2_score".
meta_cond: logical - split features based on meta conditions

Value

Data frame

See also

GenomicRanges::seqlengths how to set sequence information on GRanges object to preserve correct ranges.