bacsnp.filter | R Documentation |
Filtering SNP frequency dataframe
bacsnp.filter(vcfdf, min.abs.cov = 0, min.abs.alt = 0, min.rel.alt = 0)
vcfdf |
A dataframe with SNP frequencies. Data was created with vcf_transformation. |
min.abs.cov |
The minimal absolute coverage (COV) that is required to consider SNP positions. All positions with a miniam absolute coverage below this value will be removed. |
min.abs.alt |
An absolute value for the minimal number of occurances of an alternative nucleotide. |
min.rel.alt |
An relative value for the minimal frequency of an alternative nucleotide. |
A vcf dataframe that was filtered by a required minimal total coverage (COV), minimal coverage of alternative nucleotides (COV.ALT) or a minimal relative frequency of the first alterntative (REL.ALT1).
bacsnp.filter(bac, min.abs.cov = 100) bacsnp.filter(bac, min.abs.cov = 100, min.abs.alt = 10) bacsnp.filter(bac, min.abs.cov = 100, min.abs.alt = 10, min.rel.alt = 0.05) bacsnp.filter(bac, min.rel.alt = 0.05)
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