FindMaxRepeatIns: Return the number of repeat units in which an insertion is...

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Description

Return the number of repeat units in which an insertion is embedded.

Usage

FindMaxRepeatIns(context, rep.unit.seq, pos)

Arguments

context	A string into which rep.unit.seq was inserted at position pos.
rep.unit.seq	The inserted sequence and candidate repeat unit sequence.
pos	rep.unit.seq is understood to be inserted between positions pos and pos + 1.

Details

For example

rep.unit.seq = ac
pos = 2
context = xyaczt
return 1

rep.unit.seq = ac
pos = 4
context = xyaczt
return 1

rep.unit.seq = cgct
pos = 2
rep.unit.seq = at
return 0

context = gacacacacg
rep.unit.seq = ac
pos = any of 1, 3, 5, 7, 9
return 4

If substr(context, pos, pos + nchar(rep.unit.seq) - 1) != rep.unit.seq, then stop.

Value

If same sequence as rep.unit.seq occurs ending at pos or starting at pos + 1 then the number of repeat units before the insertion, otherwise 0.

ICAMS documentation built on April 3, 2021, 5:07 p.m.