Summary statistics for RADseq data

Source: R/summary_rad.R

Summarise the tidy or gds data. The summary statistics is by default calculated by strata and markers. Frequency of the REF/ALT alleles, the observed and the expected heterozygosity and the inbreeding coefficient (FIS).

summary_rad(data, path.folder = NULL, digits = 4, verbose = TRUE)

Arguments

data

(4 options) A file or object generated by radiator:

  • tidy data

  • Genomic Data Structure (GDS)

How to get GDS and tidy data ? Look into tidy_genomic_data, read_vcf or tidy_vcf.

path.folder

(path, optional) By default will print results in the working directory. Default: path.folder = NULL.

digits

(integer, optional). Default: digits = 4.

verbose

(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.