getMutationFeatureVector: Get mutation feature vector from context sequence data and...

In USCbiostats/HiLDA: Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation

Description

Get mutation feature vector from context sequence data and reference and alternate allele information

Usage

getMutationFeatureVector(
  context,
  ref_base,
  alt_base,
  strandInfo = NULL,
  numBases,
  type
)

Arguments

context	the context sequence data around the mutated position. This shoud be Biostrings::DNAStringSet class
ref_base	the reference bases at the mutated position.
alt_base	the alternate bases at the mutated position.
strandInfo	transcribed strand information at the mutated position. (this is optional)
numBases	the number of flanking bases around the mutated position.
type	the type of mutation feature vecotr (should be "independent" or "full").

Value

a mutation featuer vector

USCbiostats/HiLDA documentation built on Oct. 15, 2021, 10:22 a.m.