Description Usage Arguments Value
View source: R/snp-selection.R
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.
1 | compile_assayable(w, minMAF = 0.03, flank = 20)
|
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. |
This returns a data frame with the columns:
snp num_gene_copies
freq
scaffold
bp
length
leftpos
rightpos
leftpad
rightpad
assayable
on_right_edge
on_left_edge
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