Calculate kmer frequency in mutated and non-mutated sites. Apply fisher test
1 | kmer_freq(dataset, ks = 5, pval_cutoff = 0.001, n_keep = 80)
|
dataset |
Granges object, with a 'sequence.pyr' column containing sequence region and 'mut.pyr' column containing mutations |
ks |
Int. Size of kmers to look for |
pval_cutoff. |
Real. Filtering threshold for fisher test |
n_keep. |
Int. Number of kmers to keep |
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