NEWS.md

In surh/HMVAR: Human Microbiome Variant Analysis in R

0.1-3

0.1-2

1. Discard rows in closest files that have a dot (.) in the gene id column.
2. Added background values for gsea.
3. Added rer_functional_enrichments.r executable script.
4. Made map optional in read_midas_data.
5. Added qp_genotypes function.
6. Added mktest function that works on allele table.
7. Added find_singletons and test_singleton_enrichment functions.
8. Function qp_genotypes returns empty tibble when no sample passes.
9. Function read_eggnog deals with UHGG format.
10. Adding read_midas_info function.

0.1-1

1. Overall cleaning and NAMESPACE update
2. Adding focal group map pre-processing option for midas_mktest function and mktest,r executable script.
3. Flipping mice imputation matrix. Added support for blocks. NEED TO DOCUMENT block_size
4. Reverting to standard alphanumeric names for chromosomes in BIMBAM format.
5. Eliminating annoying messages from read_midas_abun.
6. Adding toy example in MIDAS format (Issue https://github.com/surh/HMVAR/issues/6).
7. Updating read_midas_data function, and adding examples.
8. Function midas_mktest now accepts either a file path to map or a data frame witht the map. It also has examples.
9. Examples for functions that calculate MK contingency table.
10. Added unit testing support via testhat (Issue https://github.com/surh/HMVAR/issues/25).
11. Fixed allele asignment by determine_site_dist (Issue https://github.com/surh/HMVAR/issues/1).
12. Unit testing for functions that obtain MK contingency table.
13. Adding determine_substitution_type.
14. Adding match_freq_and_depth.
15. Adding plotgg_sacked_columns.
16. Added variable_dist_per_site.
17. Added varsites_pipeline. Updated varsites.r executable. to use this function. (Issue https://github.com/surh/HMVAR/issues/4).
18. Added plotgg_manhattan function. (Issue https://github.com/surh/HMVAR/issues/10).
19. Fixed various issues with NAMESPACE. Including removing AMOR from depends field (Issue https://github.com/surh/HMVAR/issues/13).
20. Generalizing column names for genomewide_ni.
21. Added calculate_mktable.
22. Added functions for DoS (Issue https://github.com/surh/HMVAR/issues/11).
23. Created dos.r executable (Issue https://github.com/surh/HMVAR/issues/12).
24. Gene-set enrichment analysis (gsea) function created (Issue https://github.com/surh/HMVAR/issues/18).
25. Function test_go added (Issue https://github.com/surh/HMVAR/issues/16 https://github.com/surh/HMVAR/issues/14).
26. Function terms_enrichments.
27. metawas_enrichments.r script converted into executable. annotation_enrichments.r (Issue https://github.com/surh/HMVAR/issues/15).
28. Adding sign_test function (Issue https://github.com/surh/HMVAR/issues/19), and including it in terms_enrichments (Issue https://github.com/surh/HMVAR/issues/14), and to the annotation_enrichments.r executable (Issue Issue https://github.com/surh/HMVAR/issues/15).
29. In genome_metawas.r executable. Exit if there are no two groups with at least three samples each.
30. Executable mktest.r can now handle cases when midas_dir exists but no samples match the mapping file. When this happens, it issues a warning and writes a header only output file.
31. Giving command line options to manhattan_type.r via stitch_file,r
32. Glitches in annotation_enrichments.r executable. Allowing for more annotation or closest files than input files. Also dealing with different order of files.
33. Bug fixed in dos.r when directory is passed. Print the combined results instead of last species only.
34. Added verbose option to match_freq_and_depth
35. Added window_fst & calculate_fst functions for various Fst calculations (Issue https://github.com/surh/HMVAR/issues/33).

0.1-0

1. Added exectuable script to perform mktest.
2. determine_snp_effect can handle non-coding loci.
3. Added executable to calculate and plot the number of variable and fixed positions within sample (Issue https://github.com/surh/HMVAR/issues/4)
4. Added executable to subset SNPs from MIDAS after merging (Issue https://github.com/surh/HMVAR/issues/3).
5. read_midas_data now can keep non CDS positions. (Issue https://github.com/surh/HMVAR/issues/7)
6. Added functions for metawas steps: midas_to_bimbam, gemma_kinship, and gemma_lmm.
7. Created util set of functions for internal utility functions.
8. Added mice_impute() function
9. Added benchmark imputation function and executable script.
10. Added genome_metawas.r executable script.

0.0-4

1. Added ggtree import
2. Changed name to HMVAR
3. Inititiated moving to tidyverse
4. Updated genome_wide_ni
5. Fising documentation issues
6. calculate_neutrality_index.r has been updated.
7. Added pval_qqplot functions and documentation.
8. Recoment svglite package
9. Added functions for mktest from MIDAS output

0.0-3

1. Addded script to test strains for overall SNP differentiation between aevery pair of comparisons.
2. Added script and functions for genome wide neutrality index calculations.
3. Functions and script for checking and plotting p-value distribution
4. Numerous scripts and functions for evaluating mktest results

0.0-2

1. Inputing HMQC data
2. Prevalence of HMQC data

0.0-1

1. First version.
2. Prevalence in HMMCP dataset

surh/HMVAR documentation built on Aug. 18, 2021, 1:21 a.m.