CalcFreqGt: A function to count occurences of genotypes in a genotype...
In laurentlab-mpipz/rsurvival: Process genotype data from survival experiment

Description Usage Arguments Value See Also Examples

A function to count occurences of genotypes in a genotype matrix.

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CalcFreqGt(gt, genotypic = TRUE, allelic = FALSE, absolute = TRUE,
  percentage = FALSE, totals = TRUE, backup.path = NULL,
  min.freq.gt = NULL, min.freq.al = NULL)

`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 `gt`. Variants which does not fulfill this condition will be omitted. Default is NULL (disabled).
`min.freq.al`	Optional. Minimal value of relative frequency for each allele in a variant of `gt`. Variants which does not fulfill this condition will be omitted. Default is NULL (disabled).

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

## 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)