create_data: Create data matrix for NMF

In dieterich-lab/JACUSA2helper: Post-processing for JACUSA2 output

Create data matrix for NMF

Description

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.

dieterich-lab/JACUSA2helper documentation built on March 1, 2023, 12:09 a.m.