CalcFreqVariant: A function to count occurences of genotypes in a variant...
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 variant vector.

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CalcFreqVariant(variant, genotypic = TRUE, allelic = FALSE,
  absolute = TRUE, percentage = FALSE, totals = TRUE,
  min.freq.gt = NULL, min.freq.al = NULL)

`variant`	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
`totals`	If TRUE (default), returned vector will include totals.
`min.freq.gt`	Optional. Minimal value of relative frequency for each genotype in a `variant`. If `variant` does not fulfill this condition, return NULL. Default is NULL (disabled).
`min.freq.al`	Optional. Minimal value of relative frequency for each allele in a `variant`. If `variant` does not fulfill this condition, return NULL. Default is NULL (disabled).

A vector of frequencies. Each Item is a calculated frequency for this variant. Item names depend on provided parameters. Typical item names would be "count_gt_HomoREF" (absolute frequency of homo REF genotype) or "freq_al_ALT" (relative frequency of ALT alleles). Item names ending with "MissVal" concern samples with missing values for this variant. Item names ending with "Total" concern all samples for this variant, including the ones with missing data.

CalcFreqGt which bind this function

## Not run: 
CalcFreqVariant(variant)
CalcFreqVariant(variant, genotypic = FALSE, allelic = TRUE)
CalcFreqVariant(variant, absolute = FALSE, percentage = TRUE)
CalcFreqVariant(variant, totals= FALSE, min.freq.al = 0.15)

## End(Not run)