Grape

DESCRIPTION

@@ -1,76 +1,65 @@
 Package: BIGr
-Title: Breeding Insight Genomics Functions for Polyploid and Diploid Species
-Version: 0.8.0
-Authors@R: c(person(given='Alexander M.',
-                    family='Sandercock',
-                    email='sandercock.alex@gmail.com',
-                    role=c('cre','aut')),
-             person(given='Cristiane',
-                    family='Taniguti',
-                    role = 'aut'),
-             person(given='Josue',
-                    family='Chinchilla-Vargas',
-                    role='aut'),
-             person(given='Shufen',
-                    family='Chen',
-                    role='ctb'),
-             person(given='Manoj',
-                    family='Sapkota',
-                    role='ctb'),
-             person(given='Meng',
-                    family='Lin',
-                    role='ctb'),
-             person(given='Dongyan',
-                    family='Zhao',
-                    role='ctb'),
-             person('University', "of Florida",
-                    role=c('cph'), 
-                    comment = "Breeding Insight"))
+Title: Breeding Insight Genomics Functions for Polyploid and Diploid
+    Species
+Version: 0.8.1
+Authors@R: c(
+    person("Alexander M.", "Sandercock", , "sandercock.alex@gmail.com", role = c("cre", "aut")),
+    person("Cristiane", "Taniguti", role = "aut"),
+    person("Josue", "Chinchilla-Vargas", role = "aut"),
+    person("Shufen", "Chen", role = "ctb"),
+    person("Manoj", "Sapkota", role = "ctb"),
+    person("Meng", "Lin", role = "ctb"),
+    person("Dongyan", "Zhao", role = "ctb"),
+    person("University", "of Florida", role = "cph",
+           comment = "Breeding Insight")
+  )
 Maintainer: Alexander M. Sandercock <sandercock.alex@gmail.com>
 Description: Functions developed within Breeding Insight to analyze
     diploid and polyploid breeding and genetic data. 'BIGr' provides the
-    ability to filter variant call format (VCF) files, extract single nucleotide polymorphisms (SNPs) 
-    from diversity arrays technology missing allele discovery count (DArT MADC) files, 
-    and manipulate genotype data for both diploid and polyploid species. It
-    also serves as the core dependency for the 'BIGapp' 'Shiny' app, which
-    provides a user-friendly interface for performing routine genotype
-    analysis tasks such as dosage calling, filtering, principal component analysis (PCA), 
-    genome-wide association studies (GWAS), and
-    genomic prediction. For more details about the included 'breedTools' 
-    functions, see Funkhouser et al. (2017) <doi:10.2527/tas2016.0003>, and
-    the 'updog' output format, see Gerard et al. (2018) <doi:10.1534/genetics.118.301468>.
+    ability to filter variant call format (VCF) files, extract single
+    nucleotide polymorphisms (SNPs) from diversity arrays technology
+    missing allele discovery count (DArT MADC) files, and manipulate
+    genotype data for both diploid and polyploid species. It also serves
+    as the core dependency for the 'BIGapp' 'Shiny' app, which provides a
+    user-friendly interface for performing routine genotype analysis tasks
+    such as dosage calling, filtering, principal component analysis (PCA),
+    genome-wide association studies (GWAS), and genomic prediction. For
+    more details about the 'updog' output
+    format, see Gerard et al. (2018) <doi:10.1534/genetics.118.301468>.
 License: Apache License (>= 2)
 URL: https://github.com/Breeding-Insight/BIGr
 BugReports: https://github.com/Breeding-Insight/BIGr/issues
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-Depends: R (>= 4.4.0)
-biocViews:
+Depends: 
+    R (>= 4.4.0)
 Imports: 
-    parallel,
+    Biostrings,
     dplyr,
+    ggplot2,
+    parallel,
+    pwalign,
     Rdpack (>= 0.7),
     readr (>= 2.1.5),
     reshape2 (>= 1.4.4),
     rlang,
-    tidyr (>= 1.3.1),
-    vcfR (>= 1.15.0),
     Rsamtools,
-    Biostrings,
-    pwalign,
-    janitor,
-    quadprog,
-    tibble,
+    stats,
     stringr,
-    data.table
+    tibble,
+    tidyr (>= 1.3.1),
+    utils,
+    vcfR (>= 1.15.0)
 Suggests: 
+    testthat (>= 3.0.0),
     covr,
-    ggplot2,
     spelling,
-    rmdformats,
-    knitr (>= 1.10),
-    rmarkdown,
     polyRAD,
-    testthat (>= 3.0.0)   
-RdMacros: Rdpack
+    rmdformats,
+    knitr,
+    rmarkdown
+RdMacros: 
+    Rdpack
+biocViews:
 Config/roxygen2/version: 8.0.0
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3

NAMESPACE

@@ -1,17 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
-export(allele_freq_poly)
 export(calculate_Het)
 export(calculate_MAF)
 export(check_homozygous_trios)
 export(check_madc_sanity)
-export(check_ped)
 export(check_replicates)
 export(dosage2vcf)
 export(dosage_ratios)
 export(filterMADC)
 export(filterVCF)
-export(find_parentage)
 export(flip_dosage)
 export(get_countsMADC)
 export(imputation_concordance)
@@ -20,13 +17,10 @@ export(madc2vcf_all)
 export(madc2vcf_multi)
 export(madc2vcf_targets)
 export(merge_MADCs)
-export(solve_composition_poly)
 export(thinSNP)
 export(updog2vcf)
-export(validate_pedigree)
 import(dplyr)
 import(parallel)
-import(quadprog)
 import(stringr)
 import(tibble)
 import(tidyr)
@@ -35,32 +29,16 @@ importFrom(Biostrings,DNAString)
 importFrom(Biostrings,reverseComplement)
 importFrom(Rdpack,reprompt)
 importFrom(Rsamtools,bgzip)
-importFrom(data.table,CJ)
-importFrom(data.table,as.data.table)
-importFrom(data.table,copy)
-importFrom(data.table,data.table)
-importFrom(data.table,fread)
-importFrom(data.table,is.data.table)
-importFrom(data.table,rbindlist)
-importFrom(data.table,set)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
 importFrom(dplyr,arrange)
-importFrom(dplyr,bind_rows)
 importFrom(dplyr,case_when)
-importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
-importFrom(dplyr,first)
 importFrom(dplyr,group_by)
 importFrom(dplyr,group_modify)
-importFrom(dplyr,if_else)
 importFrom(dplyr,mutate)
-importFrom(dplyr,n)
-importFrom(dplyr,n_distinct)
-importFrom(dplyr,row_number)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
-importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,where)
 importFrom(ggplot2,aes)
@@ -70,14 +48,12 @@ importFrom(ggplot2,ggplot)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_minimal)
-importFrom(janitor,clean_names)
 importFrom(pwalign,nucleotideSubstitutionMatrix)
 importFrom(pwalign,pairwiseAlignment)
 importFrom(readr,read_csv)
 importFrom(reshape2,dcast)
 importFrom(reshape2,melt)
 importFrom(rlang,sym)
-importFrom(stats,cor)
 importFrom(stats,reorder)
 importFrom(stats,setNames)
 importFrom(tibble,as_tibble)

NEWS.md

@@ -1,3 +1,9 @@
+# BIGr 0.8.1
+
+- Updated madc2vcf_all and madc2vcf_targets. Before, it was possible for POS to be exported as scientific notation instead of integers, and for negative POS values to be present for off target SNPs. POS are corrected to be integers, and SNPs with a negative POS value are removed.
+- Remove BIGpopA functions - now it is a independent package: https://github.com/Breeding-Insight/BIGpopA 
+- Fixed `madc2vcf_all()` error "invalid substring arguments" that occurred with `add_others = TRUE` when an off-target ("Other") allele aligned to the reference with no mismatch positions remaining after the target SNP position was removed. The reference/alternate base lookups for off-target alleles are now guarded by the existing non-empty check, matching how the off-target Match alleles are already handled.
+
 # BIGr 0.7.2
 
 - Fixed manual text errors