dartR (version 1.9.9.1)

gl.play.history: Replays the history and applies it to a genlight object

Description

Replays the history and applies it to a genlight object

Usage

gl.play.history(x, history = NULL, verbose = 0)

Arguments

x

-- a genlight object [with a history slot [optional]]

history

-- [optional]. If no history is provided the complete history of x is used (recreating the identical object x). If history is a vector it indicates which which part of the history of x is used [c(1,3,4) uses the first, third and forth entry from x@other$history]. Or a simple link to a history slot of another genlight object (e.g. codex2@other$history[c(1,4,5)]).

verbose

[default 0]. If set to one then history commands are printed, which may facilitate reading the output.

Value

returns a genlight object that was created by replaying the provided applied to the genlight object x. Please note you can "mix" histories or part of them and apply them to different genlight objects. If the history does not contain gl.read.dart, histories of x and history are concatenated.

Details

This function basically allows to create a "template history" (=set of filters) and apply them to any other genlight object. Histories can also be saved and loaded (see. gl.save.history and gl.load.history).

Examples

# NOT RUN {
dartfile <- system.file("extdata","testset_SNPs_2Row.csv", package="dartR")
metadata <- system.file("extdata","testset_metadata.csv", package="dartR")
gl <- gl.read.dart(dartfile, ind.metafile = metadata, probar=FALSE) 
gl2 <- gl.filter.callrate(gl, method="loci", threshold=0.9)
gl3 <- gl.filter.callrate(gl2, method="ind", threshold=0.95)
#Now "replay" part of the history "onto" another genlight object
bc.fil <- gl.play.history(gl.compliance.check(bandicoot.gl), 
history=gl3@other$history[c(2,3)], verbose=1)
gl.print.history(bc.fil)
# }