parallel.core
argument for some internal functions to help windows users with parallel processing problems in R. #188.DynamicClusterCall
pushed greavess #189pcadapt
, 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;)snp.ld
: using missing data now works by chromosome/scaffold.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.run_bayescan
to run BayeScan ... with radiatorwrite
functions also included in genomic_converter
: write_bayescan
, write_pcadapt
and write_hzar
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