BLMM: Block length of the missing motif.

In svilsen/STRMPS: Analysis of Short Tandem Repeat (STR) Massively Parallel Sequencing (MPS) Data

Description

Given a motif length and a string it finds the blocks of the string.

Usage

BLMM(s, motifLength = 4, returnType = "numeric")

Arguments

s	a string of either class: 'character' or 'DNAString'.
motifLength	the known motif length of the STR region.
returnType	the type of return wanted. Takes three values 'numeric', 'string', or 'fullList' (or any other combination cased letters).

Details

If returnType is 'numeric', the function returns the numeric value of the LUS. If returnType is instead chosen as 'string', the function returns "[AATG]x" i.e. the motif, AATG, is repeated 'x' times. Lastly if the returnType is set to fullList, the function returns a list of data.frames containing every possible repeat structure their start and the numeric value of the repeat unit length.

Value

Depending on returnType it return an object of class 'numeric', 'string', or 'fulllist'.

Examples

# Creating compound string 's'
stretch1 = paste0(rep("AATG", 10), collapse = "")
stretch2 = paste0(rep("ATCG", 4), collapse = "")

s = paste0(stretch1, stretch2)

# Return BLMM only
BLMM(s, motifLength = 4, returnType = "numeric")

# Return BLMM and motif of stretch
BLMM(s, motifLength = 4, returnType = "string")

# Return all blocks of 's'
BLMM(s, motifLength = 4, returnType = "fulllist")

svilsen/STRMPS documentation built on May 31, 2019, 7:55 a.m.