NEWS.md
pcadapt, bayescan, genlight output thanks to @jcaccavo. Confusion between POP_ID and STRATA remained for some less used functions while the migration towards STRATA only inside radiator.filter_ma that now incorporate Minor Allele Frequency (MAF), Minor Allele Count (MAC) and Minor Allele Depth (MAD).genomic_converter
genomic_converter when using genlight as input and PLINK as output filetidyr::gather and tidyr::spread dependencies (they are deprecated)data.table melt function. Changed to tidyr::pivot_long.fineRADstructure rules have changed, I’m no longer doing gymnastic to make the population work with genomic_converter or write_fineradstructure, it’s not up to the user to make sure the pop id starts with a letter. Some codes might now be broken because of this.read_plink and tidy_plink: new rules to get the best out of PLINK tped and bed files.detect_microsatellites: new radiator function that detect microsatellites using GMATA.genepopedit and rubias
detect_paralogs that copy the method described in McKinney et al. 2017. This function is the logical step to make available for users after detect_mixed_genomes, filter_hwe and sexy_markers.sexy_markers: couple of bug fixed. More testing with the different genomic format.SeqArray and GDS integrationradiator and now lives exclusively in package grur
filter_dart is deprecated. Please use filter_rad, the ONE function to rule them all;)tidy_vcf, tidy_genomic_data and genomic_converter: works better with ipyrad vcf’stidy_vcf, tidy_genomic_data and genomic_converter: works better with freebayes and stacks vcftidy_vcf, tidy_genomic_data and genomic_converter: work without strata/pop groupingsnp_ld: new argument ld.threshold for long.distance linkage disequilibrium.write_vcf: will now output ID as LOCUS_COL or LOCUS_(POS-1) if COL info is not provided.tidy_vcf, tidy_genomic_data and genomic_converter: way faster with huge VCFtidy_vcf and write_seqarray: work better with vcf generated by Stackswrite_ldna: new function that generates a LDna input file from a tidy data frame.tidy_vcf, tidy_genomic_data and genomic_converter: way faster with huge VCFwrite_fineradstructure: fix bug when data was from DArTgenomic_converter, tidy_genomic_data: bug fix when individuals are integersfis_summary: arguments updatedfilter_dart and filter_rad: can now opt out of HWE filtering.filter_hwe: user can opt to see figures but skip filteringwrite_gsi_sim from assigner to radiatorwrite functions: write_snprelate and write_seqarray
radiator dependencies, several packages were moved in the Suggests field.filter_dart: lots of new stuff. More appropriate filter arguments:
filter.coverage is deprecated in favour of: filter.markers.coveragefilter.ind.missing.geno is deprecated in favour of: filter.markers.missing
erase.genotypes: new argument tailored to handle coverage for DArT counts data.filter.individuals.missing: allows to blacklist sample early in the filtering pipeline.radiator is ready for stacks v.2 beta8data.table to increase speed during melting or casting data framestidy_genomic_data and genomic_converter: bug fix and improvements.write_snprelate and it’s associated output from genomic_converter is no longer available because of difficulties students are having in installing the package, it’s dependencies and/or using the output. The code remains available here, without support.radiator::snp.ld: the module inside tidy_genomic_data and genomic_converter to minimize short linkage disequilibrium as a new option snp.ld = "middle". For locus with > 2 SNPs/read the option allows to select at random one SNP between the first and the last SNP on the read. If the locus as <= 2 SNPs on the read, the first one is selected. Note that for that last option, the numbers are reported. Thanks to Ido Bar for the idea.tidy_dart and filter_dart:
* at the beginning of certain lines).tidy_genomic_data and genomic_converter can now accept DArT data directly.