Extract Differential Abundance Results
Source:R/analysis_result_extractors.R
extract_differential_abundance_result.RdReturn the tidy result table from a differential_abundance_result object.
Examples
data("global_patterns", package = "microbiomedataset")
x0 <- prune_taxa(global_patterns, variable_id = global_patterns@variable_info$variable_id[1:120])
genus_object <- summarise_taxa(x0, taxonomic_rank = "Genus")
result_table <- data.frame(
variable_id = genus_object@variable_info$variable_id[1:6],
estimate = seq(-1, 1, length.out = 6)
)
x <- create_differential_abundance_result(
result = cbind(result_table, genus_object@variable_info[1:6, ]),
taxonomic_rank = "Genus"
)
head(extract_differential_abundance_result(x))
#> variable_id estimate variable_id Kingdom
#> 1 Sulfolobus -1.0 Sulfolobus Archaea
#> 2 Cenarchaeum -0.6 Cenarchaeum Archaea
#> 3 Nitrosopumilus -0.2 Nitrosopumilus Archaea
#> 4 CandidatusNitrososphaera 0.2 CandidatusNitrososphaera Archaea
#> 5 Natronococcus 0.6 Natronococcus Archaea
#> 6 Natronorubrum 1.0 Natronorubrum Archaea
#> Phylum Class Order Family
#> 1 Crenarchaeota Thermoprotei Sulfolobales Sulfolobaceae
#> 2 Crenarchaeota Thaumarchaeota Cenarchaeales Cenarchaeaceae
#> 3 Crenarchaeota Thaumarchaeota Cenarchaeales Cenarchaeaceae
#> 4 Crenarchaeota Thaumarchaeota Nitrososphaerales Nitrososphaeraceae
#> 5 Euryarchaeota Halobacteria Halobacteriales Halobacteriaceae
#> 6 Euryarchaeota Halobacteria Halobacteriales Halobacteriaceae
#> Genus Species p_value q_value
#> 1 Sulfolobus Sulfolobusacidocaldarius NA NA
#> 2 Cenarchaeum <NA> NA NA
#> 3 Nitrosopumilus <NA> NA NA
#> 4 CandidatusNitrososphaera CandidatusNitrososphaeragargensis NA NA
#> 5 Natronococcus <NA> NA NA
#> 6 Natronorubrum <NA> NA NA
#> direction
#> 1 negative
#> 2 negative
#> 3 negative
#> 4 positive
#> 5 positive
#> 6 positive