indexSNPs: Obtain the index of SNPs inside a block with defined size

In poolABC: Approximate Bayesian Computation with Pooled Sequencing Data

Obtain the index of SNPs inside a block with defined size

Description

Selects a random block of a smaller size from a larger contig and obtain the index of the SNPs that are contained within that block.

Usage

indexSNPs(positions, range, window)

Arguments

positions	is a numeric vector where each entry corresponds to the position of a SNP present in the contig.
range	is a numeric vector with two entries: the first is the minimum position of any SNP of the contig and the second is the maximum position of any SNP in that same contig.
window	is a non-negative integer indicating the size, in base pairs, of the block of the contig to keep.

Details

This function starts by removing the edges of the contig. The size of the removed portion is equal to the size of the block to keep. Then, a SNP is randomly pick from the vector of all possible SNP positions. An initial block is constructed by selecting all SNPs contained in a window of window size, both upstream and downstream from that SNP. Finally, SNPs are removed from both ends of that initial block until all remaining SNPs are contained within a block of window size.

Value

a numeric vector containing the index of the SNPs present within a randomly selected window of a given contig.

poolABC documentation built on Aug. 8, 2023, 5:14 p.m.