Extract Cross-Omics Association Results
Source:R/analysis_result_extractors.R
extract_association_result.RdReturn the tidy association table from a
microbe_metabolite_association object.
Examples
data("demo_crossomics", package = "microbiomedataset")
x <- calculate_correlation(
microbiome_data = demo_crossomics$microbiome_data,
metabolome_data = demo_crossomics$metabolome_data,
sample_link = demo_crossomics$sample_link,
metabolome_transform = "none"
)
head(extract_association_result(x))
#> taxon_id metabolite_id estimate p_value n_samples q_value
#> 1 Blautia_A CADAVERINE 0.07958667 0.625433219 40 0.9442916
#> 2 Blautia_A _1_METHYLXANTHINE 0.44323514 0.004177719 40 0.5576252
#> 3 Blautia_A DHEA_S 0.11069418 0.495156030 40 0.9377717
#> 4 Blautia_A GLYCOCHOLATE 0.15214231 0.348660063 40 0.9252912
#> 5 Blautia_A PIPERINE 0.10520883 0.518217055 40 0.9405171
#> 6 Blautia_A _4_ACETAMIDOPHENOL -0.11765810 0.469645524 40 0.9309772
#> direction taxonomic_rank method
#> 1 positive Genus spearman
#> 2 positive Genus spearman
#> 3 positive Genus spearman
#> 4 positive Genus spearman
#> 5 positive Genus spearman
#> 6 negative Genus spearman
#> lineage_microbiome
#> 1 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A
#> 2 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A
#> 3 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A
#> 4 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A
#> 5 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A
#> 6 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A
#> Kingdom_microbiome Phylum_microbiome Class_microbiome Order_microbiome
#> 1 Bacteria Firmicutes_A Clostridia Lachnospirales
#> 2 Bacteria Firmicutes_A Clostridia Lachnospirales
#> 3 Bacteria Firmicutes_A Clostridia Lachnospirales
#> 4 Bacteria Firmicutes_A Clostridia Lachnospirales
#> 5 Bacteria Firmicutes_A Clostridia Lachnospirales
#> 6 Bacteria Firmicutes_A Clostridia Lachnospirales
#> Family_microbiome Genus_microbiome Species_microbiome source_study_microbiome
#> 1 Lachnospiraceae Blautia_A <NA> SINHA_CRC_2016
#> 2 Lachnospiraceae Blautia_A <NA> SINHA_CRC_2016
#> 3 Lachnospiraceae Blautia_A <NA> SINHA_CRC_2016
#> 4 Lachnospiraceae Blautia_A <NA> SINHA_CRC_2016
#> 5 Lachnospiraceae Blautia_A <NA> SINHA_CRC_2016
#> 6 Lachnospiraceae Blautia_A <NA> SINHA_CRC_2016
#> source_study_metabolome compound_name_annotation hmdb_id_annotation
#> 1 SINHA_CRC_2016 CADAVERINE HMDB0002322
#> 2 SINHA_CRC_2016 _1_METHYLXANTHINE HMDB0010738
#> 3 SINHA_CRC_2016 DHEA_S HMDB0001032
#> 4 SINHA_CRC_2016 GLYCOCHOLATE HMDB0000138
#> 5 SINHA_CRC_2016 PIPERINE HMDB0029377
#> 6 SINHA_CRC_2016 _4_ACETAMIDOPHENOL HMDB0001859
#> kegg_id_annotation annotation_level_annotation source_study_annotation
#> 1 C01672 high_confidence SINHA_CRC_2016
#> 2 <NA> high_confidence SINHA_CRC_2016
#> 3 C04555 high_confidence SINHA_CRC_2016
#> 4 C01921 high_confidence SINHA_CRC_2016
#> 5 C03882 high_confidence SINHA_CRC_2016
#> 6 <NA> high_confidence SINHA_CRC_2016
#> pathway_id_annotation pathway_name_annotation
#> 1 <NA> <NA>
#> 2 <NA> <NA>
#> 3 <NA> <NA>
#> 4 <NA> <NA>
#> 5 <NA> <NA>
#> 6 <NA> <NA>