Description Usage Arguments Value See Also Examples
A function to count occurences of genotypes in a genotype matrix.
1 2 3 |
gt |
The genotype matrix to analyse |
genotypic |
If TRUE (default), include frequencies of genotypes in the result |
allelic |
If TRUE, include frequencies of alles in the result, default set to FALSE |
absolute |
If TRUE (default), occurences will be shown instead of relative frequencies |
percentage |
If TRUE and absolute is FALSE, show the relative frequencies in percentage. Default is FALSE. |
totals |
If TRUE (default), returned vector will include totals. |
backup.path |
Optional. Path to the CSV backup file the result must be saved to. |
min.freq.gt |
Optional. Minimal value of relative frequency for each
genotype in a variant of |
min.freq.al |
Optional. Minimal value of relative frequency for each
allele in a variant of |
A data frame of frequencies. Each row is a variant and each column is a calculated frequency. Column names depend on provided parameters. Typical column names would be "count_gt_HomoREF" (absolute frequency of homo REF genotype) or "freq_al_ALT" (relative frequency of ALT alleles). Column names ending with "MissVal" concern samples with missing values for this variant. Column names ending with "Total" concern all samples for this variant, including the ones with missing data.
CalcFreqVariant
which this function bind
1 2 3 4 5 6 7 8 | ## Not run:
CalcFreqGt(genotype)
CalcFreqGt(genotype, genotypic = FALSE, allelic = TRUE)
CalcFreqGt(genotype, absolute = FALSE, percentage = TRUE)
CalcFreqGt(genotype, backup.path = "example.csv")
CalcFreqGt(genotype, totals= FALSE, min.freq.al = 0.15)
## End(Not run)
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