getflank2: Extract a specified region of the (human) genome

In STRAH: Short Tandem Repeats Analysis of Hotspot Zones

Description

This function extracts a specified region of the human genome with corresponding start and end position of the region under study.

Usage

getflank2(species, chrs, start.position, end.position)

Arguments

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).
chrs	A string reflecting the chromosome under study (starting with "chr" and adding either the integers from 1-22 or "X" respectively "Y"). 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.

Value

The DNA-sequence of the region under study (defined by the chromosome, start position, and end position) is returned.

Author(s)

Philipp Hermann, [e-mail], Monika Heinzl, [e-mail] 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

See Also

STR_analysis

Examples

getflank2(BSgenome.Hsapiens.UCSC.hg19::Hsapiens, "chr1", 1, 6)

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