dartR (version 1.9.9.1)

gl.report.taglength: Report summary of sequence tag length across loci in a genlight adegenet object

Description

SNP datasets generated by DArT typically have sequence tag lengths ranging from 20 to 69 base pairs.

Usage

gl.report.taglength(x, boxplot = "adjusted", range = 1.5, verbose = NULL)

Arguments

x

-- name of the genlight object containing the SNP data [required]

boxplot

-- if 'standard', plots a standard box and whisker plot; if 'adjusted', plots a boxplot adjusted for skewed distributions [default 'adjusted']

range

-- specifies the range for delimiting outliers [default = 1.5 interquartile ranges]

verbose

-- verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

Value

-- dataframe with loci that are outliers

Details

The minimum, maximum and mean of tag length are provided. Output also is a histogram of tag length, accompanied by a box and whisker plot presented either in standard (boxplot="standard") or adjusted for skewness (boxplot=adjusted).

Refer to Tukey (1977, Exploratory Data Analysis. Addison-Wesley) for standard Box and Whisker Plots and Hubert & Vandervieren (2008), An Adjusted Boxplot for Skewed Distributions, Computational Statistics & Data Analysis 52:5186-5201) for adjusted Box and Whisker Plots.

Examples

# NOT RUN {
out <- gl.report.taglength(testset.gl)
# }