Files in StevisonLab/genotypeR
SNP Genotype Marker Design and Analysis
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/CO.R
R/GoldenGate2iCOM_design.R
R/Heterogametic_Genotype_Warnings.R
R/Ref_Alt_Table.R
R/S4.R
R/SequenomMarkers_v3.R
R/binary_coding.R
R/convert2qtl_table.R
R/count_CO.R
R/genotypes_data.R
R/grep_df_subset.R
R/illumina_Genotype_Table.R
R/initialize_genotypeR_data.R
R/make_marker_names.R
R/markers.R
R/read_Master_SNPs_Data.R
R/read_in_illumina_GoldenGate.R
R/read_in_sequenom_data.R
R/sort_sequenom_df.R
R/subsetChromosome.R
R/zero_one_two_coding.R
README.md
data/genotypes_data.rda
data/markers.rda
genotypeR.Rproj
inst/CITATION
inst/SequenomMarkers/FS14_test.vcf
inst/SequenomMarkers/FS16_test.vcf
inst/SequenomMarkers/Finding_SNPs_GoldenGate.pl
inst/SequenomMarkers/Finding_SNPs_Sequenom.pl
inst/SequenomMarkers/Finding_SNPs_new.pl
inst/SequenomMarkers/Grandmaster_SNPs.pl
inst/SequenomMarkers/Grandmaster_new.pl
inst/SequenomMarkers/Pipeline_Rapper.sh
inst/SequenomMarkers/README.md
inst/SequenomMarkers/R_Pipeline_Rapper.sh
inst/SequenomMarkers/SequenomMarkers_Rscript_example.R
inst/SequenomMarkers_v2/README.md
inst/SequenomMarkers_v2/pop_sample/Finding_SNPs_pop_sample.pl
inst/SequenomMarkers_v2/pop_sample/Grandmaster_SNPs_pop_sample.pl
inst/SequenomMarkers_v2/pop_sample/Pipeline_rapper_pop_sample.sh
inst/SequenomMarkers_v2/pop_sample/README.md
inst/SequenomMarkers_v2/pop_sample/R_Pipeline_rapper_pop_sample.sh
inst/SequenomMarkers_v2/pop_sample/test_files/Pop_sample.vcf.zip
inst/SequenomMarkers_v2/pop_sample/test_files/Sample1.vcf
inst/SequenomMarkers_v2/pop_sample/test_files/Sample2.vcf
inst/SequenomMarkers_v2/two_sample/Finding_SNPs_two_sample.pl
inst/SequenomMarkers_v2/two_sample/Grandmaster_SNPs_two_sample.pl
inst/SequenomMarkers_v2/two_sample/Pipeline_rapper_two_sample.sh
inst/SequenomMarkers_v2/two_sample/README.md
inst/SequenomMarkers_v2/two_sample/R_Pipeline_rapper_two_sample.sh
inst/SequenomMarkers_v2/two_sample/sort_by_chr.sh
inst/SequenomMarkers_v2/two_sample/test_files/Sample1.vcf
inst/SequenomMarkers_v2/two_sample/test_files/Sample1_v_Sample2.out.diff.sites_in_files
inst/SequenomMarkers_v2/two_sample/test_files/Sample2.vcf
inst/extdata/filtered_markers.txt
inst/extdata/sequenom_test_data.csv
inst/get_SequenomMarkers_and_remove_git.sh
man/CO.Rd
man/GoldenGate2iCOM_design.Rd
man/Heterogametic_Genotype_Warnings.Rd
man/Ref_Alt_Table.Rd
man/SequenomMarkers.Rd
man/binary_coding.Rd
man/convert2qtl_table.Rd
man/count_CO.Rd
man/genotypeR-class.Rd
man/genotypes_data.Rd
man/grep_df_subset.Rd
man/illumina_Genotype_Table.Rd
man/initialize_genotypeR_data.Rd
man/make_marker_names.Rd
man/markers.Rd
man/read_in_Master_SNPs_data.Rd
man/read_in_illumina_GoldenGate.Rd
man/read_in_sequenom_data.Rd
man/sort_sequenom_df.Rd
man/subsetChromosome.Rd
man/zero_one_two_coding.Rd
tests/testthat.R
tests/testthat/test-1_binary_multi_coding.R
tests/testthat/test-2_subsetChromosome.R
tests/testthat/test-3_CO.R
tests/testthat/test-4_count_CO.R
tests/testthat/test-5_Heterogametic_Genotype_Warnings.R
tests/testthat/test-6_initialize_genotypeR_data.R
tests/testthat/test-7_sort_sequenom_df.R
tests/testthat/test_data_generator.R
vignettes/genotypeR.Rmd
vignettes/genotypeR[exported].pdf
vignettes/temp_cross_for_qtl.csv
