RAD_score: RAD_score

Description Usage Arguments

Description

Theoretically the position of backsplice junctions should be distributed randomly across a amplicon. This function calculates the read alignment distribution (RAD) of backsplice junctions between forward and reverse read pairs. The RAD score is calculated from CIGAR strings which can be used to identify type II and type III alignments.

Usage

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RAD_score(
  CIGAR_1stSeg = NULL,
  CIGAR_2ndSeg = NULL,
  RADcountThreshold = 10,
  digits = 2
)

Arguments

CIGAR_1stSeg

: CIGAR string of the first segment.

CIGAR_2ndSeg

: CIGAR string of the second segment

RADcountThreshold

: Minimum count threshold required to apply RAD score. If there are less than this many entries in CIGAR list then -1 is returned.

digits

: rounding of the RAD score to this many digits (default 2)


VCCRI/Ularcirc documentation built on July 3, 2020, 9:57 a.m.