vignettes/get_started.Rmd
get_started.Rmdvignettes/life_cycle.Rmd
life_cycle.Rmdvignettes/rad_genomics_computer_setup.Rmd
rad_genomics_computer_setup.Rmd
NEWS.md
+ tidyr::gather and tidyr::spread dependencies (they are deprecated)data.table melt function. Changed to tidyr::pivot_long.Assign the default values for...
-assign_defaults(n, verbose = TRUE, pos = 1)+
assign_defaults(n, env.arg, verbose = TRUE)diff --git a/docs/reference/bayescan_one.html b/docs/reference/bayescan_one.html index e07654e2..7401119b 100644 --- a/docs/reference/bayescan_one.html +++ b/docs/reference/bayescan_one.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/betas_estimator.html b/docs/reference/betas_estimator.html index b9788d34..b547565e 100644 --- a/docs/reference/betas_estimator.html +++ b/docs/reference/betas_estimator.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/blacklist_hw.html b/docs/reference/blacklist_hw.html index 03a3fbba..02c368e7 100644 --- a/docs/reference/blacklist_hw.html +++ b/docs/reference/blacklist_hw.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/boxplot_stats.html b/docs/reference/boxplot_stats.html index 677308f8..a94ec4c6 100644 --- a/docs/reference/boxplot_stats.html +++ b/docs/reference/boxplot_stats.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/calibrate_alleles.html b/docs/reference/calibrate_alleles.html index 8ff425cb..85475fd3 100644 --- a/docs/reference/calibrate_alleles.html +++ b/docs/reference/calibrate_alleles.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/change_pop_names.html b/docs/reference/change_pop_names.html index 6223810f..82446752 100644 --- a/docs/reference/change_pop_names.html +++ b/docs/reference/change_pop_names.html @@ -74,7 +74,7 @@ diff --git a/docs/reference/check_args_class.html b/docs/reference/check_args_class.html index d4131952..dfdab645 100644 --- a/docs/reference/check_args_class.html +++ b/docs/reference/check_args_class.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/check_dart.html b/docs/reference/check_dart.html index f50e3535..531cd0d4 100644 --- a/docs/reference/check_dart.html +++ b/docs/reference/check_dart.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/check_header_source_vcf.html b/docs/reference/check_header_source_vcf.html index 820ae759..3500465d 100644 --- a/docs/reference/check_header_source_vcf.html +++ b/docs/reference/check_header_source_vcf.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/check_pop_levels.html b/docs/reference/check_pop_levels.html index 97f0b8ac..cfcc53eb 100644 --- a/docs/reference/check_pop_levels.html +++ b/docs/reference/check_pop_levels.html @@ -73,7 +73,7 @@ diff --git a/docs/reference/clean_ad.html b/docs/reference/clean_ad.html index 4bc47540..f26363b6 100644 --- a/docs/reference/clean_ad.html +++ b/docs/reference/clean_ad.html @@ -73,7 +73,7 @@ diff --git a/docs/reference/clean_dart_colnames.html b/docs/reference/clean_dart_colnames.html index 3c769198..703cfdd8 100644 --- a/docs/reference/clean_dart_colnames.html +++ b/docs/reference/clean_dart_colnames.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/clean_dart_locus.html b/docs/reference/clean_dart_locus.html index 23938417..85ef3e59 100644 --- a/docs/reference/clean_dart_locus.html +++ b/docs/reference/clean_dart_locus.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/clean_gl.html b/docs/reference/clean_gl.html index 2d64b840..30fb9878 100644 --- a/docs/reference/clean_gl.html +++ b/docs/reference/clean_gl.html @@ -73,7 +73,7 @@ diff --git a/docs/reference/clean_ind_names.html b/docs/reference/clean_ind_names.html index ef2dd65d..fae59fb4 100644 --- a/docs/reference/clean_ind_names.html +++ b/docs/reference/clean_ind_names.html @@ -77,7 +77,7 @@ diff --git a/docs/reference/clean_markers_names.html b/docs/reference/clean_markers_names.html index 8f347371..ef388a0c 100644 --- a/docs/reference/clean_markers_names.html +++ b/docs/reference/clean_markers_names.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/clean_nr.html b/docs/reference/clean_nr.html index 6c83e5e7..9ead84f4 100644 --- a/docs/reference/clean_nr.html +++ b/docs/reference/clean_nr.html @@ -73,7 +73,7 @@ diff --git a/docs/reference/clean_nv.html b/docs/reference/clean_nv.html index 2a3c92f2..55aeae1d 100644 --- a/docs/reference/clean_nv.html +++ b/docs/reference/clean_nv.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/clean_pl.html b/docs/reference/clean_pl.html index 9ba052ef..984d2043 100644 --- a/docs/reference/clean_pl.html +++ b/docs/reference/clean_pl.html @@ -77,7 +77,7 @@ diff --git a/docs/reference/clean_pop_names.html b/docs/reference/clean_pop_names.html index 736848ce..6c9f06ab 100644 --- a/docs/reference/clean_pop_names.html +++ b/docs/reference/clean_pop_names.html @@ -76,7 +76,7 @@ diff --git a/docs/reference/compound_assignment_pipe_operator.html b/docs/reference/compound_assignment_pipe_operator.html index c90b7481..e6b4992c 100644 --- a/docs/reference/compound_assignment_pipe_operator.html +++ b/docs/reference/compound_assignment_pipe_operator.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/compute_mac.html b/docs/reference/compute_mac.html index 203c9765..c40e8281 100644 --- a/docs/reference/compute_mac.html +++ b/docs/reference/compute_mac.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/compute_maf.html b/docs/reference/compute_maf.html index 8ce88d5f..76ffabbc 100644 --- a/docs/reference/compute_maf.html +++ b/docs/reference/compute_maf.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/count_monomorphic.html b/docs/reference/count_monomorphic.html index bf0c2136..cbdc4ae7 100644 --- a/docs/reference/count_monomorphic.html +++ b/docs/reference/count_monomorphic.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/dart2gds.html b/docs/reference/dart2gds.html index bc03fb36..b014b21b 100644 --- a/docs/reference/dart2gds.html +++ b/docs/reference/dart2gds.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/data_info.html b/docs/reference/data_info.html index a1b11a8d..e1af76a7 100644 --- a/docs/reference/data_info.html +++ b/docs/reference/data_info.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/detect_all_missing.html b/docs/reference/detect_all_missing.html index ec8cf663..9d45de96 100644 --- a/docs/reference/detect_all_missing.html +++ b/docs/reference/detect_all_missing.html @@ -74,7 +74,7 @@ diff --git a/docs/reference/detect_allele_problems.html b/docs/reference/detect_allele_problems.html index ae96792e..1e5e2953 100644 --- a/docs/reference/detect_allele_problems.html +++ b/docs/reference/detect_allele_problems.html @@ -80,7 +80,7 @@ diff --git a/docs/reference/detect_biallelic_markers.html b/docs/reference/detect_biallelic_markers.html index ef1f211f..58e64355 100644 --- a/docs/reference/detect_biallelic_markers.html +++ b/docs/reference/detect_biallelic_markers.html @@ -74,7 +74,7 @@ diff --git a/docs/reference/detect_biallelic_problems.html b/docs/reference/detect_biallelic_problems.html index 399cec50..ae4c6999 100644 --- a/docs/reference/detect_biallelic_problems.html +++ b/docs/reference/detect_biallelic_problems.html @@ -76,7 +76,7 @@ diff --git a/docs/reference/detect_dart_format.html b/docs/reference/detect_dart_format.html index ace1f0bd..43a3b982 100644 --- a/docs/reference/detect_dart_format.html +++ b/docs/reference/detect_dart_format.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/detect_duplicate_genomes.html b/docs/reference/detect_duplicate_genomes.html index 41676228..c72e8b5d 100644 --- a/docs/reference/detect_duplicate_genomes.html +++ b/docs/reference/detect_duplicate_genomes.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/detect_genomic_format.html b/docs/reference/detect_genomic_format.html index b25a8a65..5f2b500c 100644 --- a/docs/reference/detect_genomic_format.html +++ b/docs/reference/detect_genomic_format.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/detect_het_outliers.html b/docs/reference/detect_het_outliers.html index 2be0bbc3..6bb708d6 100644 --- a/docs/reference/detect_het_outliers.html +++ b/docs/reference/detect_het_outliers.html @@ -76,7 +76,7 @@ diff --git a/docs/reference/detect_microsatellites.html b/docs/reference/detect_microsatellites.html index 44c6d139..9871b7fb 100644 --- a/docs/reference/detect_microsatellites.html +++ b/docs/reference/detect_microsatellites.html @@ -75,7 +75,7 @@ diff --git a/docs/reference/detect_mixed_genomes.html b/docs/reference/detect_mixed_genomes.html index af602516..1bafb958 100644 --- a/docs/reference/detect_mixed_genomes.html +++ b/docs/reference/detect_mixed_genomes.html @@ -74,7 +74,7 @@ diff --git a/docs/reference/detect_paralogs.html b/docs/reference/detect_paralogs.html index ff4d10c4..e84dbea1 100644 --- a/docs/reference/detect_paralogs.html +++ b/docs/reference/detect_paralogs.html @@ -77,7 +77,7 @@ diff --git a/docs/reference/detect_ref_genome.html b/docs/reference/detect_ref_genome.html index 7426bbd1..f9134363 100644 --- a/docs/reference/detect_ref_genome.html +++ b/docs/reference/detect_ref_genome.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/diagnostic_maf.html b/docs/reference/diagnostic_maf.html index 4a767c2f..c21e83cf 100644 --- a/docs/reference/diagnostic_maf.html +++ b/docs/reference/diagnostic_maf.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/discard_monomorphic_markers.html b/docs/reference/discard_monomorphic_markers.html deleted file mode 100644 index 3162ed12..00000000 --- a/docs/reference/discard_monomorphic_markers.html +++ /dev/null @@ -1,193 +0,0 @@ - - - - - - - - -
R/radiator_deprecated_functions.R
- discard_monomorphic_markers.RdDiscard monomorphic markers. -Used internally in radiator -and might be of interest for users.
-discard_monomorphic_markers(data, verbose = FALSE)- -
| data | -A tidy data frame object in the global environment or
-a tidy data frame in wide or long format in the working directory.
-How to get a tidy data frame ?
-Look into radiator |
-
|---|---|
| verbose | -(optional, logical) |
-
A list with the filtered input file and the blacklist of markers removed.
- -Extract and Assign ...
-extract_dots(n, v, verbose = TRUE, pos = 1)+
extract_dots(n, v, env.arg, verbose = TRUE)diff --git a/docs/reference/extract_genotypes_metadata.html b/docs/reference/extract_genotypes_metadata.html index 3bae261b..6ff8c2c6 100644 --- a/docs/reference/extract_genotypes_metadata.html +++ b/docs/reference/extract_genotypes_metadata.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/extract_individuals_metadata.html b/docs/reference/extract_individuals_metadata.html index 0ecb6516..18527753 100644 --- a/docs/reference/extract_individuals_metadata.html +++ b/docs/reference/extract_individuals_metadata.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/extract_individuals_vcf.html b/docs/reference/extract_individuals_vcf.html index 675d4de6..c3777aa3 100644 --- a/docs/reference/extract_individuals_vcf.html +++ b/docs/reference/extract_individuals_vcf.html @@ -74,7 +74,7 @@ diff --git a/docs/reference/extract_info_vcf.html b/docs/reference/extract_info_vcf.html index 2f37c3e8..b63bee95 100644 --- a/docs/reference/extract_info_vcf.html +++ b/docs/reference/extract_info_vcf.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/extract_markers_metadata.html b/docs/reference/extract_markers_metadata.html index 373ea1f3..7a8b1634 100644 --- a/docs/reference/extract_markers_metadata.html +++ b/docs/reference/extract_markers_metadata.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/filter_blacklist_genotypes.html b/docs/reference/filter_blacklist_genotypes.html index 824a50ec..cb77a748 100644 --- a/docs/reference/filter_blacklist_genotypes.html +++ b/docs/reference/filter_blacklist_genotypes.html @@ -75,7 +75,7 @@ diff --git a/docs/reference/filter_common_markers.html b/docs/reference/filter_common_markers.html index f447f1bc..5ed21971 100644 --- a/docs/reference/filter_common_markers.html +++ b/docs/reference/filter_common_markers.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/filter_coverage.html b/docs/reference/filter_coverage.html index dc67dcc4..e80f4e04 100644 --- a/docs/reference/filter_coverage.html +++ b/docs/reference/filter_coverage.html @@ -76,7 +76,7 @@ diff --git a/docs/reference/filter_dart_reproducibility.html b/docs/reference/filter_dart_reproducibility.html index e4ba9fc0..866fa418 100644 --- a/docs/reference/filter_dart_reproducibility.html +++ b/docs/reference/filter_dart_reproducibility.html @@ -75,7 +75,7 @@ diff --git a/docs/reference/filter_fis.html b/docs/reference/filter_fis.html index dcca907c..5f6f5f36 100644 --- a/docs/reference/filter_fis.html +++ b/docs/reference/filter_fis.html @@ -72,7 +72,7 @@ diff --git a/docs/reference/filter_genotyping.html b/docs/reference/filter_genotyping.html index b09f743e..5e7eddd4 100644 --- a/docs/reference/filter_genotyping.html +++ b/docs/reference/filter_genotyping.html @@ -75,7 +75,7 @@ diff --git a/docs/reference/filter_het.html b/docs/reference/filter_het.html index 31ee09ee..c707f849 100644 --- a/docs/reference/filter_het.html +++ b/docs/reference/filter_het.html @@ -92,7 +92,7 @@ diff --git a/docs/reference/filter_hwe.html b/docs/reference/filter_hwe.html index a2296bd9..95abd7df 100644 --- a/docs/reference/filter_hwe.html +++ b/docs/reference/filter_hwe.html @@ -90,7 +90,7 @@ diff --git a/docs/reference/filter_individuals.html b/docs/reference/filter_individuals.html index a97a929a..ef8c50b8 100644 --- a/docs/reference/filter_individuals.html +++ b/docs/reference/filter_individuals.html @@ -83,7 +83,7 @@ diff --git a/docs/reference/filter_ld.html b/docs/reference/filter_ld.html index ecbfcba9..469bd553 100644 --- a/docs/reference/filter_ld.html +++ b/docs/reference/filter_ld.html @@ -92,7 +92,7 @@ diff --git a/docs/reference/filter_mac.html b/docs/reference/filter_mac.html index 591caf1d..c3f249fd 100644 --- a/docs/reference/filter_mac.html +++ b/docs/reference/filter_mac.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/filter_maf.html b/docs/reference/filter_maf.html index af39ca03..df301b09 100644 --- a/docs/reference/filter_maf.html +++ b/docs/reference/filter_maf.html @@ -75,7 +75,7 @@ diff --git a/docs/reference/filter_monomorphic.html b/docs/reference/filter_monomorphic.html index bfbd83ac..b7e13625 100644 --- a/docs/reference/filter_monomorphic.html +++ b/docs/reference/filter_monomorphic.html @@ -84,7 +84,7 @@ diff --git a/docs/reference/filter_rad.html b/docs/reference/filter_rad.html index 7bcc60b5..e8d83a61 100644 --- a/docs/reference/filter_rad.html +++ b/docs/reference/filter_rad.html @@ -75,7 +75,7 @@ @@ -197,8 +197,12 @@
output = c("genind", "genepop", "structure"), to have preferred
-output formats generated. With default, only the tidy format is generated.
-Default: output = NULL.
+output formats generated. With default, only the tidy format is generated.
+Make sure to read the particularities of each format, some might +requires extra columns in the strata file. You can find the info in the +corresponding write_ functions of radiator +(reference).
+Default: output = NULL.
output = c("genind", "genepop", "structure"), to have preferred
-output formats generated. With default, only the tidy format is generated.
-Default: output = NULL.
+output formats generated. With default, only the tidy format is generated.
+Make sure to read the particularities of each format, some might +requires extra columns in the strata file. You can find the info in the +corresponding write_ functions of radiator +(reference).
+Default: output = NULL.
filter DArT file
Individual filter
Population filter
(optional, tibble file or object) This tibble of individual's
metadata must contain
-four colums: SAMPLE_TYPE, REPUNIT, COLLECTION, INDIVIDUALS. Those columns
+four columns: SAMPLE_TYPE, REPUNIT, COLLECTION, INDIVIDUALS. Those columns
are described in rubias.
Default:strata = NULL. With default, SAMPLE_TYPE is filled
with reference. REPUNIT and COLLECTION will be filled by
diff --git a/docs/reference/write_snprelate.html b/docs/reference/write_snprelate.html
index 61d31494..785b2815 100644
--- a/docs/reference/write_snprelate.html
+++ b/docs/reference/write_snprelate.html
@@ -75,7 +75,7 @@
diff --git a/docs/reference/write_stockr.html b/docs/reference/write_stockr.html
index 8ecabd67..87762273 100644
--- a/docs/reference/write_stockr.html
+++ b/docs/reference/write_stockr.html
@@ -74,7 +74,7 @@
diff --git a/docs/reference/write_structure.html b/docs/reference/write_structure.html
index 6b8c62c6..5f349eb4 100644
--- a/docs/reference/write_structure.html
+++ b/docs/reference/write_structure.html
@@ -75,7 +75,7 @@
diff --git a/docs/reference/write_vcf.html b/docs/reference/write_vcf.html
index b6bf997a..49314286 100644
--- a/docs/reference/write_vcf.html
+++ b/docs/reference/write_vcf.html
@@ -75,7 +75,7 @@
diff --git a/man/.DS_Store b/man/.DS_Store
new file mode 100644
index 00000000..5008ddfc
Binary files /dev/null and b/man/.DS_Store differ
diff --git a/man/discard_monomorphic_markers.Rd b/man/discard_monomorphic_markers.Rd
deleted file mode 100644
index d2552073..00000000
--- a/man/discard_monomorphic_markers.Rd
+++ /dev/null
@@ -1,30 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/radiator_deprecated_functions.R
-\name{discard_monomorphic_markers}
-\alias{discard_monomorphic_markers}
-\title{Discard monomorphic markers}
-\usage{
-discard_monomorphic_markers(data, verbose = FALSE)
-}
-\arguments{
-\item{data}{A tidy data frame object in the global environment or
-a tidy data frame in wide or long format in the working directory.
-\emph{How to get a tidy data frame ?}
-Look into \pkg{radiator} \code{\link{tidy_genomic_data}}.}
-
-\item{verbose}{(optional, logical) \code{verbose = TRUE} to be chatty
-during execution.
-Default: \code{verbose = FALSE}.}
-}
-\value{
-A list with the filtered input file and the blacklist of markers removed.
-}
-\description{
-Discard monomorphic markers.
-Used internally in \href{https://github.com/thierrygosselin/radiator}{radiator}
-and might be of interest for users.
-}
-\author{
-Thierry Gosselin \email{thierrygosselin@icloud.com}
-}
-\keyword{internal}
diff --git a/man/filter_dart.Rd b/man/filter_dart.Rd
deleted file mode 100644
index 5e9a0fff..00000000
--- a/man/filter_dart.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/radiator_deprecated_functions.R
-\name{filter_dart}
-\alias{filter_dart}
-\title{filter DArT file}
-\usage{
-filter_dart(...)
-}
-\arguments{
-\item{...}{Read life cycle section below}
-}
-\description{
-Use \code{\link{filter_rad}}.
-}
-\section{Life cycle}{
-
-
-As of radiator v.0.0.22, \code{filter_dart} is now replaced by
-\code{\link{filter_rad}} in an effort to have more meaningful functions names.
-This is THE function to rule them all.
-}
-
diff --git a/man/filter_individual.Rd b/man/filter_individual.Rd
deleted file mode 100644
index cc82388f..00000000
--- a/man/filter_individual.Rd
+++ /dev/null
@@ -1,162 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/radiator_deprecated_functions.R
-\name{filter_individual}
-\alias{filter_individual}
-\title{Individual filter}
-\usage{
-filter_individual(
- interactive.filter = TRUE,
- data,
- strata = NULL,
- ind.approach = "pop",
- ind.threshold = 0.5,
- prob.pop.threshold = 0,
- percent = FALSE,
- filename = NULL,
- parallel.core = parallel::detectCores() - 1,
- ...
-)
-}
-\arguments{
-\item{interactive.filter}{(optional, logical) Do you want the filtering session to
-be interactive. With default: \code{interactive.filter == TRUE}, the user is
-asked to see figures of distribution before making decisions for filtering.}
-
-\item{data}{14 options for input (\strong{diploid data only}): VCFs (SNPs or Haplotypes,
-to make the vcf population ready),
-plink (tped, bed), stacks haplotype file, genind (library(adegenet)),
-genlight (library(adegenet)), gtypes (library(strataG)), genepop, DArT,
-and a data frame in long/tidy or wide format. To verify that radiator detect
-your file format use \code{\link{detect_genomic_format}} (see example below).
-Documented in \strong{Input genomic datasets} of \code{\link{tidy_genomic_data}}.
-
-\strong{DArT and VCF data}: \pkg{radiator} was not meant to generate alleles
-and genotypes if you are using a VCF file with no genotype
-(only genotype likelihood: GL or PL).
-Neither is \pkg{radiator} able to magically generate a genind object
-from a SilicoDArT dataset. Please look at the first few lines of your dataset
-to understand it's limit before asking raditor to convert or filter your dataset.}
-
-\item{strata}{(optional)
-The strata file is a tab delimited file with a minimum of 2 columns headers:
-\code{INDIVIDUALS} and \code{STRATA}. Documented in \code{\link{read_strata}}.
-DArT data: a third column \code{TARGET_ID} is required.
-Documented on \code{\link{read_dart}}. Also use the strata read function to
-blacklist individuals.
-Default: \code{strata = NULL}.}
-
-\item{ind.approach}{(character).
-The approach to filter a marker, is it based on the overall number of
-genotyped individuals (no concept of populations here),
-\code{ind.approach = "overall"}, or
-the number of genotyped individuals per population \code{ind.approach = "pop"}.
-Default: \code{ind.approach = "pop"}.}
-
-\item{ind.threshold}{The individual threshold, proportion, percentage or
-number e.g. 0.70, 70, 15.
-Default: \code{ind.threshold = 0.5}.}
-
-\item{prob.pop.threshold}{(integer, optional) Useful to incorporate problematic
-populations dragging down polymorphism discovery, but still wanted for analysis.
-If individuals with missing genotypes are not managed upstream,
-use this threshold to allow variance in the number of populations passing
-the \code{ind.threshold} argument. e.g. with \code{prob.pop.threshold = 2},
-you tolerate a maximum of 2 populations failing to pass the
-\code{ind.threshold}. Manage after the problematic populations
-downstream with blacklist of individuals and/or missing data imputations. This
-argument is not necessary with \code{ind.approach = "overall"}.
-Default: \code{prob.pop.threshold = 0}. See details for more info.}
-
-\item{percent}{Is the threshold a percentage? TRUE or FALSE.
-This argument is necessary to distinguish percentage from integer individual
-threshold (e.g. 70 percent or 70 individuals).
-Default: \code{percent = FALSE}.}
-
-\item{filename}{(optional) The function uses \code{\link[fst]{write.fst}},
-to write the tidy data frame in
-the folder created in the working directory. The file extension appended to
-the \code{filename} provided is \code{.rad}.
-Default: \code{filename = NULL}.}
-
-\item{parallel.core}{(optional) The number of core used for parallel
-execution during import.
-Default: \code{parallel.core = parallel::detectCores() - 1}.}
-
-\item{...}{(optional) To pass further arguments for fine-tuning the function.}
-}
-\value{
-With \code{interactive.filter = FALSE}, a list in the global environment,
-with 7 objects:
-\enumerate{
-\item $tidy.filtered.ind
-\item $whitelist.markers
-\item $blacklist.markers
-\item $strata
-\item $filters.parameters
-}
-
-With \code{interactive.filter = TRUE}, a list with 2 additionnal objects is created.
-\enumerate{
-\item $plot.ind.threshold
-\item $ind.threshold.helper.table
-}
-
-The object can be isolated in separate object outside the list by
-following the example below.
-}
-\description{
-Filter individuals genotyped at a marker from a tidy data
-set (long format) of any of these file format:
-vcf, plink (tped/tfam), stacks haplotype file, genind,
-genepop, data frame in wide format. The function uses
-\code{\link[radiator]{tidy_genomic_data}} and
-\code{\link[radiator]{tidy_wide}} to load the file. For filtering
-you can consider the overall number of individuals (no concept of populations here),
-or the number of genotyped individuals per pop. The threshold can be a fixed
-number of individuals, a proportion or a percentage.
-}
-\details{
-\strong{Interactive version}
-
-There is 2 steps in the interactive version to visualize and filter
-the data based on the number of genotyped individuals:
-
-Step 1. Impact of individual threshold on marker discovery
-
-Step 2. Choose the filtering approach and thresholds
-
-
-
-\strong{prob.pop.threshold}
-
-If your a regular radiator user, you've seen the \code{pop.num.threshold}.
-\code{prob.pop.threshold}, is a bit different and requires more thinking,
-because the number of populations genotyped potentially vary across markers,
-which make difficult, sometimes, the use of \code{pop.num.threshold}.
-e.g. If only 2 populations out of 10 are genotyped for a marker and you use
-\code{pop.num.threshold = 0.6} this could lead to inconsistensis. Thus,
-it's easier to use the number of population you are willing to accept
-failling to conform to the threshold.
-}
-\examples{
-\dontrun{
-turtle.ind <- filter_individual(
-data = "turtle.vcf",
-strata = "turtle.strata.tsv",
-ind.approach = "pop",
-ind.threshold = 50,
-percent = TRUE,
-prob.pop.threshold = 2,
-filename = "tidy.data.turtle"
-)
-
-#If interactive.filter = TRUE, a list is created and to view the filtered tidy data:
-tidy.data <- turtle.ind$tidy.filtered.ind
-
-#Inside the same list, to isolate the blacklist.genotypes:
-bg <- turtle.ind$blacklist.genotypes
-
-# The remaining argument are used in tidy_genomic_data during import and allow
-# the user to apply some filtering or selection before doing the filtering.
-}
-}
diff --git a/man/filter_population.Rd b/man/filter_population.Rd
deleted file mode 100644
index 576d7f97..00000000
--- a/man/filter_population.Rd
+++ /dev/null
@@ -1,125 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/radiator_deprecated_functions.R
-\name{filter_population}
-\alias{filter_population}
-\title{Population filter}
-\usage{
-filter_population(
- interactive.filter = TRUE,
- data,
- pop.threshold = 100,
- percent = TRUE,
- filename = NULL,
- strata = NULL,
- parallel.core = parallel::detectCores() - 1,
- ...
-)
-}
-\arguments{
-\item{interactive.filter}{(optional, logical) Do you want the filtering session to
-be interactive. With default: \code{interactive.filter == TRUE}, the user is
-asked to see figures of distribution before making decisions for filtering.}
-
-\item{data}{14 options for input (\strong{diploid data only}): VCFs (SNPs or Haplotypes,
-to make the vcf population ready),
-plink (tped, bed), stacks haplotype file, genind (library(adegenet)),
-genlight (library(adegenet)), gtypes (library(strataG)), genepop, DArT,
-and a data frame in long/tidy or wide format. To verify that radiator detect
-your file format use \code{\link{detect_genomic_format}} (see example below).
-Documented in \strong{Input genomic datasets} of \code{\link{tidy_genomic_data}}.
-
-\strong{DArT and VCF data}: \pkg{radiator} was not meant to generate alleles
-and genotypes if you are using a VCF file with no genotype
-(only genotype likelihood: GL or PL).
-Neither is \pkg{radiator} able to magically generate a genind object
-from a SilicoDArT dataset. Please look at the first few lines of your dataset
-to understand it's limit before asking raditor to convert or filter your dataset.}
-
-\item{pop.threshold}{The population threshold, proportion, percentage or
-number e.g. 0.70, 70, 15.
-Default: \code{pop.threshold = 100}.}
-
-\item{percent}{Is the threshold a percentage? TRUE or FALSE.
-This argument is necessary to distinguish percentage from integer population
-threshold (e.g. 50 percent or 50 populations).
-Default: \code{percent = TRUE}.}
-
-\item{filename}{(optional) The function uses \code{\link[fst]{write.fst}},
-to write the tidy data frame in
-the folder created in the working directory. The file extension appended to
-the \code{filename} provided is \code{.rad}.
-Default: \code{filename = NULL}.}
-
-\item{strata}{(optional)
-The strata file is a tab delimited file with a minimum of 2 columns headers:
-\code{INDIVIDUALS} and \code{STRATA}. Documented in \code{\link{read_strata}}.
-DArT data: a third column \code{TARGET_ID} is required.
-Documented on \code{\link{read_dart}}. Also use the strata read function to
-blacklist individuals.
-Default: \code{strata = NULL}.}
-
-\item{parallel.core}{(optional) The number of core used for parallel
-execution during import.
-Default: \code{parallel.core = parallel::detectCores() - 1}.}
-
-\item{...}{(optional) To pass further arguments for fine-tuning the function.}
-}
-\value{
-With \code{interactive.filter = FALSE}, a list in the global environment,
-with 7 objects:
-\enumerate{
-\item $tidy.filtered.ind
-\item $whitelist.markers
-\item $blacklist.markers
-\item $strata
-\item $filters.parameters
-}
-
-With \code{interactive.filter = TRUE}, a list with 2 additionnal objects is created.
-\enumerate{
-\item $plot.pop.threshold
-\item $pop.threshold.helper.table
-}
-
-The object can be isolated in separate object outside the list by
-following the example below.
-}
-\description{
-Filter markers based on populations genotyped. Use a tidy data
-set (long format) of any of these file format:
-vcf, plink (tped/tfam), stacks haplotype file, genind,
-genepop, data frame in wide format. The function uses
-\code{\link[radiator]{tidy_genomic_data}} and
-\code{\link[radiator]{tidy_wide}} to load the file. For filtering
-The threshold can be a fixed number of population, a proportion or a percentage.
-}
-\details{
-\strong{Interactive version}
-
-There is 2 steps in the interactive version to visualize and filter
-the data based on the population representation:
-
-Step 1. Impact of population threshold on marker discovery
-
-Step 2. Choose the filtering threshold
-}
-\examples{
-\dontrun{
-turtle.pop <- filter_population(
-data = "turtle.vcf",
-strata = "turtle.strata.tsv",
-pop.thresholds = 100,
-percent = TRUE,
-filename = "tidy.data.turtle.tsv"
-)
-
-#If interactive.filter = TRUE, a list is created and to view the filtered tidy data:
-tidy.data <- turtle.ind$tidy.filtered.ind
-
-#Inside the same list, to isolate the blacklist.genotypes:
-bg <- turtle.ind$blacklist.genotypes
-
-# The remaining argument are used in tidy_genomic_data during import and allow
-# the user to apply some filtering or selection before doing the filtering.
-}
-}
diff --git a/man/filter_rad.Rd b/man/filter_rad.Rd
index 727cf3cd..af8963f2 100644
--- a/man/filter_rad.Rd
+++ b/man/filter_rad.Rd
@@ -52,6 +52,12 @@ snprelate, maverick, genepopedit, rubias, hapmap and dadi.
Use a character string,
e.g. \code{output = c("genind", "genepop", "structure")}, to have preferred
output formats generated. With default, only the tidy format is generated.
+
+Make sure to read the particularities of each format, some might
+requires extra columns in the strata file. You can find the info in the
+corresponding \emph{write_} functions of radiator
+(\href{https://thierrygosselin.github.io/radiator/reference/index.html}{reference}).
+
Default: \code{output = NULL}.}
\item{filename}{(optional) The filename prefix for the objet in the global environment
diff --git a/man/genomic_converter.Rd b/man/genomic_converter.Rd
index 634d70d7..b9eb664d 100644
--- a/man/genomic_converter.Rd
+++ b/man/genomic_converter.Rd
@@ -46,6 +46,12 @@ snprelate, maverick, genepopedit, rubias, hapmap and dadi.
Use a character string,
e.g. \code{output = c("genind", "genepop", "structure")}, to have preferred
output formats generated. With default, only the tidy format is generated.
+
+Make sure to read the particularities of each format, some might
+requires extra columns in the strata file. You can find the info in the
+corresponding \emph{write_} functions of radiator
+(\href{https://thierrygosselin.github.io/radiator/reference/index.html}{reference}).
+
Default: \code{output = NULL}.}
\item{filename}{(optional) The filename prefix for the object in the global environment
diff --git a/man/keep_common_markers.Rd b/man/keep_common_markers.Rd
deleted file mode 100644
index d1d0c6e9..00000000
--- a/man/keep_common_markers.Rd
+++ /dev/null
@@ -1,43 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/radiator_deprecated_functions.R
-\name{keep_common_markers}
-\alias{keep_common_markers}
-\title{Keep markers in common between all populations}
-\usage{
-keep_common_markers(data, plot = FALSE, verbose = FALSE)
-}
-\arguments{
-\item{data}{A tidy data frame object in the global environment or
-a tidy data frame in wide or long format in the working directory.
-\emph{How to get a tidy data frame ?}
-Look into \pkg{radiator} \code{\link{tidy_genomic_data}}.}
-
-\item{plot}{(optional, logical) \code{plot = TRUE} will produce an
-\href{https://github.com/hms-dbmi/UpSetR}{UpSet plot} to visualize the number
-of markers between populations. The package is required for this to work...
-Default: \code{plot = FALSE}.}
-
-\item{verbose}{(optional, logical) \code{verbose = TRUE} to be chatty
-during execution.
-Default: \code{verbose = FALSE}.}
-}
-\value{
-A list with the filtered input data set,
-the whitelist of markers in common and the blacklist of markers discarded.
-}
-\description{
-Keep markers in common between all populations.
-Used internally in \href{https://github.com/thierrygosselin/radiator}{radiator}
-and might be of interest for users.
-}
-\section{Life cycle}{
-
-
-As of radiator v.0.0.22, keep.common.markers function is deprecated and was replaced by
-\code{\link{filter_common_markers}} in an effort to have more meaningful functions names.
-}
-
-\author{
-Thierry Gosselin \email{thierrygosselin@icloud.com}
-}
-\keyword{internal}
diff --git a/man/write_rubias.Rd b/man/write_rubias.Rd
index 7367d1e1..916236a8 100644
--- a/man/write_rubias.Rd
+++ b/man/write_rubias.Rd
@@ -25,7 +25,7 @@ Look into \code{\link{tidy_genomic_data}},
\item{strata}{(optional, tibble file or object) This tibble of individual's
metadata must contain
-four colums: \code{SAMPLE_TYPE, REPUNIT, COLLECTION, INDIVIDUALS}. Those columns
+four columns: \code{SAMPLE_TYPE, REPUNIT, COLLECTION, INDIVIDUALS}. Those columns
are described in \strong{rubias}.
Default:\code{strata = NULL}. With default, \code{SAMPLE_TYPE} is filled
with \code{reference}. \code{REPUNIT} and \code{COLLECTION} will be filled by