Reports summary of sequence tag length across loci
Source:R/gl.report.taglength.r
gl.report.taglength.Rd
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
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.pa()
,
gl.report.parent.offspring()
,
gl.report.rdepth()
,
gl.report.reproducibility()
,
gl.report.secondaries()
,
gl.report.sexlinked()
Author
Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr
Examples
out <- gl.report.taglength(testset.gl)
#> Starting gl.report.taglength
#> Processing genlight object with SNP data
#> Reporting Tag Length
#> No. of loci = 255
#> No. of individuals = 250
#> Minimum : 20
#> 1st quantile : 63
#> Median : 69
#> Mean : 60.70196
#> 3r quantile : 69
#> Maximum : 69
#> Missing Rate Overall: 0.12
#>
#> Quantile Threshold Retained Percent Filtered Percent
#> 1 100% 69 185 72.5 70 27.5
#> 2 95% 69 185 72.5 70 27.5
#> 3 90% 69 185 72.5 70 27.5
#> 4 85% 69 185 72.5 70 27.5
#> 5 80% 69 185 72.5 70 27.5
#> 6 75% 69 185 72.5 70 27.5
#> 7 70% 69 185 72.5 70 27.5
#> 8 65% 69 185 72.5 70 27.5
#> 9 60% 69 185 72.5 70 27.5
#> 10 55% 69 185 72.5 70 27.5
#> 11 50% 69 185 72.5 70 27.5
#> 12 45% 69 185 72.5 70 27.5
#> 13 40% 69 185 72.5 70 27.5
#> 14 35% 69 185 72.5 70 27.5
#> 15 30% 69 185 72.5 70 27.5
#> 16 25% 63 194 76.1 61 23.9
#> 17 20% 46 207 81.2 48 18.8
#> 18 15% 37 217 85.1 38 14.9
#> 19 10% 30 230 90.2 25 9.8
#> 20 5% 26 244 95.7 11 4.3
#> 21 0% 20 255 100.0 0 0.0
#> Completed: gl.report.taglength
#>