motif_detection: DNA-motif detection in a given DNAStringSet, a given...
In STRAH: Short Tandem Repeats Analysis of Hotspot Zones

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

This function searches for a given "DNA-motif" in a DNA-sequence. The argument seqName can be either a DNAStringSet object or it refers to a fasta-file. Additionally, we provide the option to specify a species, a chromosome, a start, and a stop position for a region of any reference genome to be analyzed. By default a region of the human genome is analyzed. Optionally, one can also specify the number of mismatches of the DNA-motif and whether the reverse complement has to be searched.

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motif_detection(seqName, chrs, start.position, end.position, motif,
  nr.mismatch = 0, reverse.comp = F, print.status = T,
  species = BSgenome.Hsapiens.UCSC.hg19::Hsapiens)

`seqName`	A character string which can either be the name of a DNAStringSet object or a sequence name referring to a fasta-file to be analyzed. This argument can only be ignored if `chr` and `start.position` and `end.position` are specified.
`chrs`	A character string reflecting the chromosome under study (starting with "chr" and adding either the integers from 1-22 or "X" respectively "Y" for the human chromosome). 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.
`motif`	A character string reflecting the specified DNA-motif to be searched for in the DNA-sequence.
`nr.mismatch`	This integer specifies the number of allowed mismatches when searching for the specified DNA-motif.
`reverse.comp`	A logical value, by default `FALSE`, which enables to search the reverse complement of the sequence if set to `TRUE`.
`print.status`	A logical value reflecting whether the current status of the worked sequence (relative to the sequence length) is printed (`TRUE`) or not (`FALSE`).
`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).

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

`Species`	The name of the species under study
`Sequence Name`	The name of the region under study
`Reverse Complement`	Indicator whether the reverse complement was searched
`Number of Matches`	The frequency of found DNA-motifs in the region under study
`Start Positions of Matches`	The start positions of the found DNA-motifs
`Number of allowed Mismatches`	The number of allowed mismatches when searching for the DNA-motif
`Matched Segments`	The list of the segments containing the DNA-motif

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

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

getflank2

data(chr6_1580213_1582559)
motif_detection(seqName = chr6_1580213_1582559, start.position = NA, end.position = NA,
motif = "CCNCCNTNNCCNC", nr.mismatch = 1, reverse.comp = FALSE, print.status = FALSE)


motif_detection(chrs = "chr6", start.position = 1580213, end.position = 1582559,
motif = "CCNCCNTNNCCNC", nr.mismatch = 1, reverse.comp = FALSE, print.status = 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")) {
motif_detection(chrs = "chr1", start.position =222339618, end.position = 222339660,
motif = "A", nr.mismatch = 0, reverse.comp = FALSE, print.status = FALSE,
species = BSgenome.Ptroglodytes.UCSC.panTro5::BSgenome.Ptroglodytes.UCSC.panTro5)
}