# Gene Set Analysis Using the Gene Set Ordinal Association Test

## Documentation for package ‘goat’ version 1.1

- DESCRIPTION file.
- Package NEWS.

## Help Pages

available_genesets_goatrepo | Discover available geneset collections from the GOAT GitHub repository
cluster_genesets | cluster significant genesets from 'test_genesets()' by geneset similarity (separately for each 'geneset source')
darken_color | naively darken a color by mixing in black
download_genesets_goatrepo | Download and parse geneset collections from the GOAT GitHub repository
download_goat_manuscript_data | Download the datasets that were used in the GOAT manuscript
filter_genesets | filter a geneset table; intersect with an array of genes-of-interest then apply cutoffs on min/max genes per geneset
gg_color_hue | generate colours analogous to ggplot's default palette
goat_logo | ASCII logo for this package
goat_nulldistributions | Precomputed parameters used by the GOAT algorithm
goat_print_version | Print package version and logo to console
goat_version | Return goat package version as a string
go_gene2go | parse gene2go file
go_obo | simple vectorized parsing of GO OBO file without any dependencies (beyond dplyr/tibble/tidyr)
hgnc_idmap_table | Parse HGNC gene identifier lookup table that was downloaded from genenames.org into a table with HGNC ID, symbol, synonym (NA if unavailable), entrez ID
lighten_color | naively lighten a color by mixing in white
load_genesets_gmtfile | parse genesets in GMT format where gene identifiers are numeric Entrez gene IDs
load_genesets_go_bioconductor | Load GO annotations via Bioconductor packages (e.g. org.Hs.eg.db for Human)
load_genesets_go_fromfile | construct a geneset table from gene2go and OBO files
load_genesets_syngo | parse genesets from the SynGO database
minlog10_fixzero | -log10 transform a vector of p-values, replacing zeros with some limit/threshold
padjust_genesets | Adjust p-values for all genesets, grouped by 'source' then adjust for the number of 'sources'
partition_genes | Classify genes into 2 groups, e.g. to define significant or topN genes, resulting in a 'signif' column with boolean values
plot_heatmap | plot the geneset similarity matrix as a heatmap
plot_lollipop | Lollipop chart or barplot visualization of geneset enrichment testing results
plot_network | plot geneset distance matrix as a network
plot_volcano | For each provided geneset, a volcano plot of all genelist log2fc and p-values with respective geneset constituents highlighted
rankscore | compute rank^2 scores and rescale these between 0~1000 (with further precision captured by decimals)
rankscore_fixed_order | Gene score array, from low to high scores
reduce_genesets | Reduce the set of significant genesets to a minimum
save_genesets | Write a geneset table to file.
score_geneset_directionality | Compute a score between -1 and 1 representing the proportion of up- or down-regulated genes for each geneset, weighted by gene effectsizes
score_geneset_oddsratio | Compute odds-ratio for each geneset
string_trunc_right | simple string truncation
symbol_to_entrez | Map the the symbol column in a table to HGNC human gene IDs by matching official gene symbols and synonyms
taxonomy_identifiers | Lookup table for taxonomy identifiers, their names and respective Bioconductor packages
test_genesets | Perform geneset enrichment testing using any supported method
test_genesets_fisherexact | Geneset ORA using Fisher-exact test
test_genesets_goat_bootstrap | Naive GOAT variant where we estimate null parameters for each geneset size independently
test_genesets_goat_fitfunction | Variant of the main GOAT function 'test_genesets_goat_precomputed' that does not use previously prepared parameters
test_genesets_goat_precomputed | Test geneset enrichment with the Geneset Ordinal Association Test (GOAT) algorithm
test_genesets_gsea | GSEA as implemented in the fgsea R package
test_genesets_hypergeometric | Geneset ORA using hypergeometric test
treemap_data | Construct tree and treemap data structures from geneset parent/child relations
treemap_plot | Plot a treemap