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Prints history of a genlight object

Usage

gl.print.history(x = NULL, history = NULL)

Arguments

x

A genlight object (with history) [optional].

history

Either a link to a history slot (gl\@other$history), or a vector indicating which part of the history of x is used [c(1,3,4) uses the first, third and forth entry from x\@other$history]. If no history is provided the complete history of x is used (recreating the identical object x) [optional].

Value

Prints a table with all history records. Currently the style cannot be changed.

Author

Bernd Gruber (bugs? Post to https://groups.google.com/d/forum/dartr)

Examples

# \donttest{
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)
#> Starting gl.read.dart 
#> Starting utils.read.dart 
#>   Topskip not provided.
#>  Setting topskip to 3 .
#>   Reading in the SNP data
#>   Detected 2 row format.
#> Number of rows per clone (should be only  2 s): 2 
#>  Added the following locus metrics:
#> AlleleID CloneID AlleleSequence SNP SnpPosition CallRate OneRatioRef OneRatioSnp TrimmedSequence FreqHomRef FreqHomSnp FreqHets PICRef PICSnp AvgPIC AvgCountRef AvgCountSnp RepAvg .
#> Recognised: 250 individuals and 255  SNPs in a 2 row format using /home/runner/work/_temp/Library/dartR/extdata/testset_SNPs_2Row.csv 
#> Completed: utils.read.dart 
#> Starting utils.dart2genlight 
#> Starting conversion....
#> Format is 2 rows.
#> Please note conversion of bigger data sets will take some time!
#> Once finished, we recommend to save the object using save(object, file="object.rdata")
#> Adding individual metrics: /home/runner/work/_temp/Library/dartR/extdata/testset_metadata.csv .
#>   Ids for individual metadata (at least a subset of) are matching!
#>   Found  250 matching ids out of 250 ids provided in the ind.metadata file.
#>   Added population assignments.
#>   Added latlon data.
#>  Added  id  to the other$ind.metrics slot.
#>   Added  pop  to the other$ind.metrics slot.
#>   Added  lat  to the other$ind.metrics slot.
#>   Added  lon  to the other$ind.metrics slot.
#>   Added  sex  to the other$ind.metrics slot.
#>   Added  maturity  to the other$ind.metrics slot.
#> Completed: utils.dart2genlight 
#>  Data read in. Please check carefully the output above
#>   Read depth calculated and added to the locus metrics
#>   Minor Allele Frequency (MAF) calculated and added to the locus metrics
#>   Recalculating locus metrics provided by DArT (optionally specified)
#> Completed: gl.read.dart 
#> 
gl2 <- gl.filter.callrate(gl, method='loc', threshold=0.9)
#> Starting gl.filter.callrate 
#>   Processing genlight object with SNP data
#>   Warning: Data may include monomorphic loci in call rate 
#>                     calculations for filtering
#>   Recalculating Call Rate
#>   Removing loci based on Call Rate, threshold = 0.9 
#> 

#> Completed: gl.filter.callrate 
#> 
gl3 <- gl.filter.callrate(gl2, method='ind', threshold=0.95)
#> Starting gl.filter.callrate 
#>   Processing genlight object with SNP data
#>   Warning: Data may include monomorphic loci in call rate 
#>                     calculations for filtering
#>   Recalculating Call Rate
#>   Removing individuals based on Call Rate, threshold = 0.95 
#>   Individuals deleted (CallRate <=  0.95 ):
#> AA032760[EmmacMDBMaci], AA019073[EmmacJohnWari], UC_00267[EmvicVictJasp], UC_00205[EmsubRopeMata], UC_00206[EmsubRopeMata], UC_00208[EmsubRopeMata], UC_00243[EmvicVictJasp], UC_00209[EmsubRopeMata], UC_00254[EmvicVictJasp], UC_00210[EmsubRopeMata], UC_00259[EmvicVictJasp], UC_00126c[EmvicVictJasp], AA063718[EmmacCoopAvin], AA063720[EmmacCoopAvin], AA063722[EmmacCoopAvin], AA063726[EmmacCoopAvin], AA063732[EmmacCoopAvin], AA063708[EmmacCoopAvin], AA063710[EmmacCoopAvin], AA063712[EmmacCoopAvin], AA063714[EmmacCoopAvin], AA063716[EmmacCoopAvin],

#>   Note: Locus metrics not recalculated
#>   Note: Resultant monomorphic loci not deleted
#> Completed: gl.filter.callrate 
#> 
#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)
# }