compile_assayable: return SNPs and say whether the are assayable or not, along...

In eriqande/genoscapeRtools: Tools for building migratory bird genoscapes

Description

This should be run on a set of data that has not been too highly filtered—you want to know if there is much variation, even if it wasn't seen in everyone.

Usage

compile_assayable(w, minMAF = 0.03, flank = 20)

Arguments

w	a matrix like produced by read_012
flank	If a SNP is to be assayable, it needs to have no SNPs within flank base pairs of itself.
MAF	the minimum minor allele frequency to retain a SNP either for assaying or for determining whether there is flanking variation.

Value

This returns a data frame with the columns:

1. snp num_gene_copies

2. freq

3. scaffold

4. bp

5. length

6. leftpos

7. rightpos

8. leftpad

9. rightpad

10. assayable

11. on_right_edge

12. on_left_edge

eriqande/genoscapeRtools documentation built on Dec. 27, 2021, 8:01 a.m.