filter_stats: Utilize all algorithms of mlg.filter

In grunwaldlab/poppr: Genetic Analysis of Populations with Mixed Reproduction

Utilize all algorithms of mlg.filter

Description

This function is a wrapper to mlg.filter. It will calculate all of the stats for mlg.filter utilizing all of the algorithms.

Usage

filter_stats(
  x,
  distance = bitwise.dist,
  threshold = 1e+06 + .Machine$double.eps^0.5,
  stats = "All",
  missing = "ignore",
  plot = FALSE,
  cols = NULL,
  nclone = NULL,
  hist = "Scott",
  threads = 1L,
  ...
)

Arguments

x	a genind, genclone, genlight, or snpclone object
distance	a distance function or matrix
threshold	a threshold to be passed to mlg.filter (Default: 1e6)
stats	what statistics should be calculated.
missing	how to treat missing data with mlg.filter
plot	If the threshold is a maximum threshold, should the statistics be plotted (Figure 2)
cols	the colors to use for each algorithm (defaults to set1 of RColorBrewer).
nclone	the number of multilocus genotypes you expect for the data. This will draw horizontal line on the graph at the value nclone and then vertical lines showing the cutoff thresholds for each algorithm.
hist	if you want a histogram to be plotted behind the statistics, select a method here. Available methods are "sturges", "fd", or "scott" (default) as documented in hist. If you don't want to plot the histogram, set hist = NULL.
threads	(unused) Previously the number of threads to be used. As of poppr version 2.4.1, this is by default set to 1.
...	extra parameters passed on to the distance function.

Value

a list of results from mlg.filter from the three algorithms. (returns invisibly if plot = TRUE)

Note

This function originally appeared in \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.17424")}

Author(s)

Zhian N. Kamvar, Jonah C. Brooks

References

ZN Kamvar, JC Brooks, and NJ Grünwald. 2015. Supplementary Material for Frontiers Plant Genetics and Genomics 'Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality'. DOI: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.17424")}

Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Front. Genet. 6:208. doi: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.3389/fgene.2015.00208")}

See Also

mlg.filter cutoff_predictor bitwise.dist diss.dist

Examples

# Basic usage example: Bruvo's Distance --------------------------------
data(Pinf)
pinfreps <- fix_replen(Pinf, c(2, 2, 6, 2, 2, 2, 2, 2, 3, 3, 2))
bres <- filter_stats(Pinf, distance = bruvo.dist, replen = pinfreps, plot = TRUE, threads = 1L)
print(bres) # shows all of the statistics

# Use these results with cutoff_filter()
print(thresh <- cutoff_predictor(bres$farthest$THRESHOLDS))
mlg.filter(Pinf, distance = bruvo.dist, replen = pinfreps) <- thresh
Pinf 

# Different distances will give different results -----------------------
nres <- filter_stats(Pinf, distance = nei.dist, plot = TRUE, threads = 1L, missing = "mean")
print(thresh <- cutoff_predictor(nres$farthest$THRESHOLDS))
mlg.filter(Pinf, distance = nei.dist, missing = "mean") <- thresh
Pinf 

grunwaldlab/poppr documentation built on March 18, 2024, 11:24 p.m.