STR_detection: Detection of short tandem repeats (STRs) in a given region of...

Description Usage Arguments Value Author(s) References See Also Examples

Description

This function searches for short tandem repeats (STRs) in a specified region of any reference genome. The parameters of the regions under study can be directly given in the function arguments or read in via either a BED-file or a position matrix. We recommend to search for STRs of minimum length 6. Options to save the output or usage of any reference genome are provided.

Usage

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STR_detection(seqName, chrs, start.position = NA, end.position = NA,
  bed_file, pos_matrix, nr.STRs, nr.mismatch = 0, reverse.comp = F,
  STR = "A", species = BSgenome.Hsapiens.UCSC.hg19::Hsapiens,
  translated_regions = F, output_file)

Arguments

seqName

A character string which is the name of the given sequence file under study. Can also be set to "" in order to analyze a defined sequence from any reference genome such as the package BSgenome.Hsapiens.UCSC.hg19 for humans.

chrs

A string reflecting the chromosome under study (starting with "chr" and adding either the integers from 1-22 or "X" respectively "Y" for the human genome). This argument can also be a vector of strings to study several chromosomes.

start.position

An integer value reflecting the start position of the region to be analyzed. If set to NA the analysis starts from the beginning of the chromosome.

end.position

An integer value reflecting the end position of the region to be analyzed. If set to NA the analysis is performed until the end of the chromosome.

bed_file

A bed file containing the chromosomes, start, and end positions of the region(s) that should be analyzed.

pos_matrix

A matrix or dataframe containing the chromosomes, start, and end positions of the region(s) that should be analyzed.

nr.STRs

An integer value as the minimum length of STRs to be detected.

nr.mismatch

An integer value reflecting the allowed number of mismatches of the short tandem repeats. By defaults set to 0.

reverse.comp

A logical value by default FALSE. If set to TRUE then the reverse complement of the sequence is analyzed.

STR

A character string for the nucleotide to be searched for. By default one searches for poly-As, hence set to "A".

species

The human genome (version 19) is default but an alternative genome can be provided. For chimpanzees the parameter has to be BSgenome.Ptroglodytes.UCSC.panTro5 (given that the data is installed).

translated_regions

A logical value by default FALSE. If set to TRUE then the function assumes that the parameters start.position and end.position were translated by some tool (e.g. liftOver) from one species to another. The untranslated and translated positions are included in the output.

output_file

The default is an empty string and does not save an output-file. The output will be saved if the parameter is changed to a user defined string excluding the extension (by default .bed).

Value

The output of the function is a list with the following content:

Sequence name

The chromosome with the start and end position of the region under study is provided. If translated_region is set to TRUE, the interval will be the translated region.

Sequence name (untranslated)

Only if translated_region is set to TRUE, then the untranslated region (chromosome with the starting and end position) is provided.

Reverse complement

An indicator whether the reverse complement was considered

Number of allowed mismatches

The number of allowed mismatches is provided.

Minimum length

The minimum length of the STR to be extracted is provided.

Number of matches

The total number of STR matches of the region is provided.

Length of STR stretch in bp

A vector containing the length of STRs per match is provided.

Start positions

The starting positions of the STRs are provided.

Matched segments

The matched segments of the STRs are provided.

A BED file with chromosomes, start, and end position of the STRs, length of the STR stretch, the matched segments, and the specified region (untranslated and translated) that was analyzed are given as columns.

Author(s)

Philipp Hermann, philipp.hermann@jku.at, Monika Heinzl, monika.heinzl@edumail.at Angelika Heissl, Irene Tiemann-Boege, Andreas Futschik

References

Heissl, A., et al. (2018) Length asymmetry and heterozygosity strongly influences the evolution of poly-A microsatellites at meiotic recombination hotspots. doi: https://doi.org/10.1101/431841

Pratto, F., et al. (2014). Recombination initiation maps of individual human genomes. Science, 346(6211).

Kuhn RM, et al. (2013) The UCSC genome browser and associated tools, Brief. Bioinform., 14, 144-161.

See Also

getflank2, STR_analysis

Examples

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data(chr6_1580213_1582559)
STR_detection(seqName = chr6_1580213_1582559, chrs = "chr6", start.position = 1580213,
end.position = 1582559, nr.STRs = 10, nr.mismatch = 0, reverse.comp = FALSE, STR = "A",
species = BSgenome.Hsapiens.UCSC.hg19::Hsapiens, translated_regions=FALSE)

STR_detection(chrs = "chr22", start.position = 30000000, end.position = 31000000,
nr.STRs = 10, nr.mismatch = 0, reverse.comp = FALSE, STR = "A",
species=BSgenome.Hsapiens.UCSC.hg19::Hsapiens, translated_regions=FALSE)
# If you want to use the function with a different reference genome
# make your choice and install it before:
if(requireNamespace("BSgenome.Ptroglodytes.UCSC.panTro5")) {
STR_detection(chrs = "chr1", start.position =222339618, end.position = 222339660,
nr.STRs = 10, nr.mismatch = 0, reverse.comp = FALSE, STR = "A",
species = BSgenome.Ptroglodytes.UCSC.panTro5::BSgenome.Ptroglodytes.UCSC.panTro5)
}

STRAH documentation built on May 2, 2019, 11:03 a.m.

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