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STRMPS

The STRMPS package is designed to extract and collect the short tandem repeat (STR) information from the fastq files produced by massively parallel sequencing (MPS).

Installation

The STRMPS-package depends on R (>= 4.4), methods, utils, tidyr, tibble, dplyr, stringr, purrr, parallel, as well as the bioconductor packages Biostrings, pwalign, ShortRead, and IRanges. Version 0.5.8 is available on CRAN, but to get the newest version devtools is needed to install the package from github.

From R, run the following commands:

install.packages("devtools")
devtools::install_github("svilsen/STRMPS")

License

This project is licensed under the MIT License.

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Version

Install

install.packages('STRMPS')

Monthly Downloads

57

Version

0.6.8

License

MIT + file LICENSE

Maintainer

Sc3<b8>ren Vilsen

Last Published

February 22nd, 2025

Functions in STRMPS (0.6.8)

findStutter,stringCoverageGenotypeList-method

Find stutters
identifySTRRegions,ShortReadQ-method

Identify the STR regions of a fastq-file or ShortReadQ-object.
identifySTRRegions,character-method

Identify the STR regions of a fastq-file or ShortReadQ-object.
stringCoverage,extractedReadsList-method

Get string coverage STR identified objects.
phredQualityScore

Convert probability to quality score
phredQualityProbability

Quality score to probability
stringCoverageList-class

A string coverage list
identifySTRRegions.control

Control function for identifySTRRegions
noiseList

Noise list
identifySTRRegions

Identify the STR regions of a fastq-file or ShortReadQ-object.
findStutter

Find stutters
stringCoverageGenotypeList

Combined string coverage and genotype information
stringCoverage,extractedReadsListNonCombined-method

Get string coverage STR identified objects.
identifyNoise

Idenfities the noise.
stringCoverage,extractedReadsListCombined-method

Get string coverage STR identified objects.
mergeGenotypeStringCoverage

Merge genotypeIdentifiedList and stringCoverageList.
mergeGenotypeStringCoverage,genotypeIdentifiedList-method

Merge genotypeIdentifiedList and stringCoverageList.
stringCoverage.control

String coverage coontrol object
stringCoverageGenotypeList-class

Combined stringCoverage- and genotypeIdentifiedList
workflow.control

Workflow default options
mergeNoiseStringCoverage,noiseIdentifiedList-method

Merge noiseIdentifiedList and stringCoverageList.
stringCoverage

Get string coverage STR identified objects.
mergeNoiseStringCoverage

Merge noiseIdentifiedList and stringCoverageList.
stringCoverage,extractedReadsListReverseComplement-method

Get string coverage STR identified objects.
stringCoverageList

Aggregated string coverage.
stringCoverageNoiseList-class

Combined stringCoverage- and noiseIdentifiedList
extractedReadsListReverseComplement-class

Extract STR region information of the reverse complement DNA strand.
findNeighbours,stringCoverageGenotypeList-method

Find neighbours
findNeighbours

Find neighbours
STRMPSWorkflow

Workflow function
extractedReadsListNonCombined-class

Combined extract STR region information.
BLMM

Block length of the missing motif.
extractedReadsListCombined-class

Combined extract STR region information.
STRMPSWorkflowCollectStutters

Collect stutters files
STRMPSWorkflowBatch

Batch wrapper for the workflow function
extractedReadsList-class

Extract STR region information
identifyNoise,stringCoverageList-method

Idenfities the noise.
getGenotype,stringCoverageList-method

Assigns genotype.
genotypeList

Genotype list
getGenotype

Assigns genotype.
genotypeIdentifiedList-class

Genotype list
flankingRegions

Flanking regions
identifiedSTRs

Identified STR regions
neighbourList-class

A neighbour list
noiseIdentifiedList-class

Noise list