gl.report.taglength {dartR} | R Documentation |
Reports summary of sequence tag length across loci
Description
SNP datasets generated by DArT typically have sequence tag lengths ranging from 20 to 69 base pairs. This function reports summary statistics of the tag lengths.
Usage
gl.report.taglength(
x,
plot.out = TRUE,
plot_theme = theme_dartR(),
plot_colors = two_colors,
save2tmp = FALSE,
verbose = NULL
)
Arguments
x |
Name of the genlight object containing the SNP [required]. |
plot.out |
If TRUE, displays a plot to guide the decision on a filter threshold [default TRUE]. |
plot_theme |
Theme for the plot. See Details for options [default theme_dartR()]. |
plot_colors |
List of two color names for the borders and fill of the plots [default two_colors]. |
save2tmp |
If TRUE, saves any ggplots and listings to the session temporary directory (tempdir) [default FALSE]. |
verbose |
Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity] |
Details
The function gl.filter.taglength
will filter out the
loci with a tag length below a specified threshold.
Quantiles are partitions of a finite set of values into q subsets of (nearly) equal sizes. In this function q = 20. Quantiles are useful measures because they are less susceptible to long-tailed distributions and outliers.
Function's output
The minimum, maximum, mean and a tabulation of tag length quantiles against thresholds are provided. Output also includes a boxplot and a histogram to guide in the selection of a threshold for filtering on tag length.
Plots and table are saved to the temporal directory (tempdir) and can be
accessed with the function gl.print.reports
and listed with
the function gl.list.reports
. Note that they can be accessed
only in the current R session because tempdir is cleared each time that the
R session is closed.
Examples of other themes that can be used can be consulted in
Value
Returns unaltered genlight object
Author(s)
Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr
See Also
gl.filter.taglength
, gl.list.reports
,
gl.print.reports
Other report functions:
gl.report.bases()
,
gl.report.callrate()
,
gl.report.diversity()
,
gl.report.hamming()
,
gl.report.heterozygosity()
,
gl.report.hwe()
,
gl.report.ld.map()
,
gl.report.locmetric()
,
gl.report.maf()
,
gl.report.monomorphs()
,
gl.report.overshoot()
,
gl.report.parent.offspring()
,
gl.report.pa()
,
gl.report.rdepth()
,
gl.report.reproducibility()
,
gl.report.secondaries()
,
gl.report.sexlinked()
Examples
out <- gl.report.taglength(testset.gl)