Preview

genotypeR-0.0.1.8.zip

StevisonLab-genotypeR-6646a4f
- .Rbuildignore 76 Bytes
- .gitignore 1.1 kB
- DESCRIPTION 1.7 kB
- NAMESPACE 898 Bytes
- R
  - CO.R 7.0 kB
  - GoldenGate2iCOM_design.R 1.9 kB
  - Heterogametic_Genotype_Warnings.R 2.4 kB
  - Ref_Alt_Table.R 2.2 kB
  - S4.R 5.9 kB
  - SequenomMarkers_v3.R 6.7 kB
  - binary_coding.R 4.7 kB
  - convert2qtl_table.R 3.6 kB
  - count_CO.R 12.0 kB
  - genotypes_data.R 565 Bytes
  - grep_df_subset.R 1.6 kB
  - illumina_Genotype_Table.R 2.7 kB
  - initialize_genotypeR_data.R 4.2 kB
  - make_marker_names.R 1.9 kB
  - markers.R 489 Bytes
  - read_Master_SNPs_Data.R 1.1 kB
  - read_in_illumina_GoldenGate.R 2.3 kB
  - read_in_sequenom_data.R 1.4 kB
  - sort_sequenom_df.R 1.8 kB
  - subsetChromosome.R 2.2 kB
  - zero_one_two_coding.R 5.0 kB
- README.md 1.5 kB
- data
  - genotypes_data.rda 2.9 kB
  - markers.rda 2.7 kB
- genotypeR.Rproj 386 Bytes
- inst
  - CITATION 1.0 kB
  - SequenomMarkers
    - FS14_test.vcf 296.0 kB
    - FS16_test.vcf 295.6 kB
    - Finding_SNPs_GoldenGate.pl 2.7 kB
    - Finding_SNPs_Sequenom.pl 2.7 kB
    - Finding_SNPs_new.pl 1.8 kB
    - Grandmaster_SNPs.pl 4.8 kB
    - Grandmaster_new.pl 2.9 kB
    - Pipeline_Rapper.sh 748 Bytes
    - README.md 2.8 kB
    - R_Pipeline_Rapper.sh 952 Bytes
    - SequenomMarkers_Rscript_example.R 315 Bytes
  - SequenomMarkers_v2
    - README.md 559 Bytes
    - pop_sample
      - Finding_SNPs_pop_sample.pl 2.5 kB
      - Grandmaster_SNPs_pop_sample.pl 3.6 kB
      - Pipeline_rapper_pop_sample.sh 544 Bytes
      - README.md 2.2 kB
      - R_Pipeline_rapper_pop_sample.sh 782 Bytes
      - test_files
        
        Pop_sample.vcf.zip 806.3 kB
        
        Sample1.vcf 385.7 kB
        
        Sample2.vcf 414.0 kB
    - two_sample
      - Finding_SNPs_two_sample.pl 3.5 kB
      - Grandmaster_SNPs_two_sample.pl 7.0 kB
      - Pipeline_rapper_two_sample.sh 771 Bytes
      - README.md 2.9 kB
      - R_Pipeline_rapper_two_sample.sh 980 Bytes
      - sort_by_chr.sh 1.2 kB
      - test_files
        
        Sample1.vcf 385.7 kB
        
        Sample1_v_Sample2.out.diff.sites_in_files 108.2 kB
        
        Sample2.vcf 414.0 kB
  - extdata
    - filtered_markers.txt 7.1 kB
    - sequenom_test_data.csv 11.0 kB
  - get_SequenomMarkers_and_remove_git.sh 239 Bytes
- man
  - CO.Rd 1.7 kB
  - GoldenGate2iCOM_design.Rd 1.5 kB
  - Heterogametic_Genotype_Warnings.Rd 1.4 kB
  - Ref_Alt_Table.Rd 676 Bytes
  - SequenomMarkers.Rd 1.3 kB
  - binary_coding.Rd 1.3 kB
  - convert2qtl_table.Rd 1.7 kB
  - count_CO.Rd 1.5 kB
  - genotypeR-class.Rd 2.1 kB
  - genotypes_data.Rd 667 Bytes
  - grep_df_subset.Rd 824 Bytes
  - illumina_Genotype_Table.Rd 1.2 kB
  - initialize_genotypeR_data.Rd 1.4 kB
  - make_marker_names.Rd 1.4 kB
  - markers.Rd 580 Bytes
  - read_in_Master_SNPs_data.Rd 841 Bytes
  - read_in_illumina_GoldenGate.Rd 1.0 kB
  - read_in_sequenom_data.Rd 1.2 kB
  - sort_sequenom_df.Rd 771 Bytes
  - subsetChromosome.Rd 1.2 kB
  - zero_one_two_coding.Rd 1.5 kB
- tests
  - testthat
    - test-1_binary_multi_coding.R 2.3 kB
    - test-2_subsetChromosome.R 1.2 kB
    - test-3_CO.R 1.2 kB
    - test-4_count_CO.R 2.0 kB
    - test-5_Heterogametic_Genotype_Warnings.R 414 Bytes
    - test-6_initialize_genotypeR_data.R 2.1 kB
    - test-7_sort_sequenom_df.R 274 Bytes
    - test_data_generator.R 2.2 kB
  - testthat.R 62 Bytes
- vignettes
  - genotypeR.Rmd 10.7 kB
  - genotypeR[exported].pdf 263.5 kB
  - temp_cross_for_qtl.csv 12.3 kB