Replays the history and applies it to a genlight object
Source:R/gl.play.history.r
gl.play.history.Rd
Replays the history and applies it to a genlight object
Arguments
- x
A genlight object (with a history slot) [optional].
- history
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 fromx@other$history
]. Or a simple link to a history slot of another genlight object (e.g. codex2@other$history[c(1,4,5)]). [optional].- verbose
If set to one then history commands are printed, which may facilitate reading the output [default 0].
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).
Author
Bernd Gruber (bugs? Post to https://groups.google.com/d/forum/dartr).
Examples
if (FALSE) { # \dontrun{
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='loc', 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)
} # }