Loads the output of [haplobreed_analysis()] — either the in-memory result or its output directory — into one object that carries the trait direction, the effective gate settings, the PCs the run adjusted for (none if it used no PCs), the tested and superior gene lists, the functional SNPs per gene, the phenotype table, and the publication-style results table. [hbr_advanced_decision()], [hbr_regate()] and [hbr_haplotype_blocks()] consume runs the same way.
Usage
hbr_read_results(
x = NULL,
trait = NULL,
phenotypes = NULL,
phenotype_id_col = "ID",
gate_params = NULL,
path = NULL,
traits = NULL
)Arguments
- x
A [haplobreed_analysis()] result, a pipeline output directory, a named character vector of directories, or a named list of results. **Alternatively**, the legacy arguments `path` and `traits` (see below) are still honoured.
- trait
Trait label; default the pipeline's stored `Trait`.
- phenotypes
Optional wide data.frame (ID column plus one column per trait, plus PC columns if the run used PCs). Needed only when the run used PCs and is read from files, because `phenotype_data_used.csv` does not carry the PC columns.
- phenotype_id_col
ID column of `phenotypes`. Default `"ID"`.
- gate_params
Optional named list overriding the stored gate settings (`alpha`, `min_d`, `min_ind`, `min_hap_freq`, `maf_min`, `trait_threshold`, `require_fdr`, `hedges`). Unspecified entries keep the values stored by the pipeline.
- path
Legacy alias: a single pipeline output directory.
- traits
Legacy alias: a named character vector of pipeline output directories, one element per trait.
Value
An object of class `hbr_run` (a list), or a named list of them classed as `hbr_run_list`. Elements of a run:
- `trait`, `direction`, `mode`
run identity and the trait direction (`"higher"` or `"lower"`)
- `gate`
effective gate settings
- `phenotype`, `pcs`, `pc_cols`
trait table and PC columns
- `gene_snps`
functional SNPs per tested gene
- `tested`, `superior`, `superior_label`
gene lists
- `table`, `table_source`
publication-style results table and the file it came from
- `summary`, `pipeline_summary`
the pipeline-summary row
Details
A single pipeline directory or result returns one `hbr_run`. A named character vector of directories or a named list of results returns one `hbr_run` per element, classed as `hbr_run_list`.
See also
[hbr_regate()] to re-apply the gate with different settings, [hbr_haplotype_blocks()] to group superior haplotypes into blocks.
Examples
toy <- system.file("extdata", "hgsi_toy", "trait_YLD",
package = "HaploBreedR")
if (nzchar(toy) && dir.exists(toy)) {
run <- hbr_read_results(toy)
run$trait
length(run$superior)
head(run$table)
}
#> Gene_ID Chr N_Functional_SNPs_Final N_Haplotypes Test P_value
#> 1 GENE01 1 3 5 ANOVA+duncan 1.586e-11
#> 2 GENE02 1 3 5 ANOVA+duncan 2.094e-02
#> 3 GENE03 1 3 4 ANOVA+duncan 1.231e-01
#> 4 GENE04 2 3 4 ANOVA+duncan 2.250e-09
#> 5 GENE05 2 3 5 ANOVA+duncan 1.504e-03
#> 6 GENE06 2 3 4 ANOVA+duncan 3.220e-01
#> Superior_Haplotype Superior_NT_Seq Superior_Mean Cohens_d Second_Haplotype
#> 1 Hap2 2-2-0 51.516 0.075 Hap4
#> 2 Hap1 2-0-0 50.548 0.098 Hap4
#> 3 Hap4 2-2-0 49.973 0.035 Hap1
#> 4 Hap3 0-0-2 52.133 0.387 Hap4
#> 5 Hap3 0-2-0 50.767 0.087 Hap4
#> 6 Hap1 0-2-0 49.874 0.006 Hap2
#> Adjusted_P Permutation_P Is_Superior gene is_superior
#> 1 1.269e-10 0.001000 FALSE GENE01 FALSE
#> 2 3.351e-02 0.020940 FALSE GENE02 FALSE
#> 3 1.407e-01 0.123100 FALSE GENE03 FALSE
#> 4 8.999e-09 0.001000 TRUE GENE04 TRUE
#> 5 3.009e-03 0.001504 FALSE GENE05 FALSE
#> 6 3.220e-01 0.322000 FALSE GENE06 FALSE