batchjacklociArp: Remove a subset of loci from all Arlequin project files...
In PopGenKit: Useful functions for (batch) file conversion and data resampling in microsatellite datasets
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Description
This function removes a specified subset of loci from all Arlequin (extension .arp) files in the working directory and creates new input .arp files. It also creates a Arlequin batch file (.arb) to allow batch analysis.
Usage
1
batchjacklociArp(rm.loci)
Arguments
rm.loci
A vector indicating which locus or loci to remove from the final output file. Loci should be indicated as numbers according to the order in which they are listed in the input file (e.g. c(1,3) would remove the first and third loci).
Details
Relies on the function jacklociArp, .
Some .arp files might not be imported correctly depending on which software was used to generate them. If this is the case, start from the Genepop files and convert them first with batchconvert or use batchconvertjack.
Value
New .arp files (with the suffix 'jackloci' in the filename) and the single batch file (.arb) will be saved in the working directory.
Author(s)
Sebastien Rioux Paquette
References
Excoffier, L. and H.E.L. Lischer (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res. 10: 564-567.
Rousset, F. (2008). Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Res. 8: 103-106.
See Also
jacklociArp, batchconvert, batchconvertjack
PopGenKit documentation built on May 2, 2019, 3:33 p.m.
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Description Usage Arguments Details Value Author(s) References See Also
Description
This function removes a specified subset of loci from all Arlequin (extension .arp) files in the working directory and creates new input .arp files. It also creates a Arlequin batch file (.arb) to allow batch analysis.
Usage
1 | batchjacklociArp(rm.loci)
|
Arguments
rm.loci |
A vector indicating which locus or loci to remove from the final output file. Loci should be indicated as numbers according to the order in which they are listed in the input file (e.g. c(1,3) would remove the first and third loci). |
Details
Relies on the function jacklociArp, .
Some .arp files might not be imported correctly depending on which software was used to generate them. If this is the case, start from the Genepop files and convert them first with batchconvert or use batchconvertjack.
Value
New .arp files (with the suffix 'jackloci' in the filename) and the single batch file (.arb) will be saved in the working directory.
Author(s)
Sebastien Rioux Paquette
References
Excoffier, L. and H.E.L. Lischer (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res. 10: 564-567.
Rousset, F. (2008). Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Res. 8: 103-106.
See Also
jacklociArp, batchconvert, batchconvertjack
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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