gbs.summary: summarize the gbs object.

In trife/gbs: Tools for Genotyping-By-Sequencing Data

Description

Processes the gbs object and calculates allele statistics. Returns allele stats, a geno object, and graphs statistics.

Usage

gbs.summary(hap, geno = F, encoding = c(-1, 0, 1), graph = F, het = "H",
  missing = "N")

Arguments

hap	The gbs object to be processed.
geno	A logical value that will convert the marker calls to a numeric geno format.
encoding	The numbers used to encode alleles (minor, het, major).
graph	A logical value that will output graphs for summary statistics (blank wells, maf, percent present, het, percent het).
het	The symbol(s) used for heterozygous calls.
missing	The symbol(s) used for missing calls.

Details

This function checks for and removes any wells that contain "blank" in the sample name, calculates allele counts, percent present, and minor allele frequency, and optionally creates a numeric geno object (stored as hap$geno). The encoding argument can be used to change how the minor, major, and heterozygous alleles are encoded. The het and missing arguments can be a character or vector to allow for multiple matches (e.g. IUPAC het = c("R","Y","S","W","K","M")).

Author(s)

Trevor Rife, [e-mail]

Jesse Poland, [e-mail]

Examples

data(wheat)
hap = gbs.summary(hap,geno=T,graph=T)

trife/gbs documentation built on May 31, 2019, 7:53 p.m.