Return the tidy result table from a crossomics_mechanism object.
Examples
data("demo_crossomics", package = "microbiomedataset")
pathway_link <- standardize_pathway_link(
data.frame(
taxon_id = summarise_taxa(
demo_crossomics$microbiome_data,
taxonomic_rank = "Genus"
)@variable_info$variable_id[1],
metabolite_id = demo_crossomics$metabolome_data@annotation_table$variable_id[1],
pathway_id = "pathway_a",
stringsAsFactors = FALSE
)
)
x <- infer_metabolic_link(
microbiome_data = demo_crossomics$microbiome_data,
metabolome_data = demo_crossomics$metabolome_data,
sample_link = demo_crossomics$sample_link,
pathway_link = pathway_link,
microbiome_rank = "Genus",
q_value_cutoff = 1
)
#> Warning: NaNs produced
head(extract_mechanism_result(x))
#> taxon_id metabolite_id estimate p_value n_samples
#> 1 Bacteroides TRICARBALLYLATE 0.6517380 5.971637e-05 33
#> 2 Blautia_A _3_7_DIMETHYLURATE 0.6935065 6.894158e-04 21
#> 3 Faecalibacterium TRYPTOPHYLPROLINE -0.6484615 6.119305e-04 25
#> 4 Coprobacter PUTRESCINE -0.6279185 7.778455e-04 25
#> 5 Dorea_A _1_METHYLXANTHINE 0.6379226 3.295862e-03 19
#> 6 Prevotella _1_METHYLXANTHINE -0.6261413 4.130492e-03 19
#> q_value direction taxonomic_rank method
#> 1 0.1718637 positive Genus spearman
#> 2 0.5464480 positive Genus spearman
#> 3 0.5464480 negative Genus spearman
#> 4 0.5464480 negative Genus spearman
#> 5 0.5545734 positive Genus spearman
#> 6 0.5638674 negative Genus spearman
#> lineage_microbiome
#> 1 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides
#> 2 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A
#> 3 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium
#> 4 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter
#> 5 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A
#> 6 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella
#> Kingdom_microbiome Phylum_microbiome Class_microbiome Order_microbiome
#> 1 Bacteria Bacteroidota Bacteroidia Bacteroidales
#> 2 Bacteria Firmicutes_A Clostridia Lachnospirales
#> 3 Bacteria Firmicutes_A Clostridia Oscillospirales
#> 4 Bacteria Bacteroidota Bacteroidia Bacteroidales
#> 5 Bacteria Firmicutes_A Clostridia Lachnospirales
#> 6 Bacteria Bacteroidota Bacteroidia Bacteroidales
#> Family_microbiome Genus_microbiome Species_microbiome source_study_microbiome
#> 1 Bacteroidaceae Bacteroides <NA> SINHA_CRC_2016
#> 2 Lachnospiraceae Blautia_A <NA> SINHA_CRC_2016
#> 3 Ruminococcaceae Faecalibacterium <NA> SINHA_CRC_2016
#> 4 Coprobacteraceae Coprobacter <NA> SINHA_CRC_2016
#> 5 Lachnospiraceae Dorea_A <NA> SINHA_CRC_2016
#> 6 Bacteroidaceae Prevotella <NA> SINHA_CRC_2016
#> source_study_metabolome compound_name_annotation.x hmdb_id_annotation.x
#> 1 SINHA_CRC_2016 TRICARBALLYLATE HMDB0031193
#> 2 SINHA_CRC_2016 _3_7_DIMETHYLURATE HMDB0001982
#> 3 SINHA_CRC_2016 TRYPTOPHYLPROLINE HMDB0029091
#> 4 SINHA_CRC_2016 PUTRESCINE HMDB0001414
#> 5 SINHA_CRC_2016 _1_METHYLXANTHINE HMDB0010738
#> 6 SINHA_CRC_2016 _1_METHYLXANTHINE HMDB0010738
#> kegg_id_annotation.x annotation_level_annotation.x source_study_annotation.x
#> 1 C19806 high_confidence SINHA_CRC_2016
#> 2 C16360 high_confidence SINHA_CRC_2016
#> 3 <NA> high_confidence SINHA_CRC_2016
#> 4 C00134 high_confidence SINHA_CRC_2016
#> 5 <NA> high_confidence SINHA_CRC_2016
#> 6 <NA> high_confidence SINHA_CRC_2016
#> pathway_id_annotation.x pathway_name_annotation.x pathway_id pathway_name
#> 1 <NA> <NA> <NA> <NA>
#> 2 <NA> <NA> <NA> <NA>
#> 3 <NA> <NA> <NA> <NA>
#> 4 <NA> <NA> <NA> <NA>
#> 5 <NA> <NA> <NA> <NA>
#> 6 <NA> <NA> <NA> <NA>
#> reaction_id reaction_name evidence_type compound_name annotation_level
#> 1 <NA> <NA> association_only <NA> <NA>
#> 2 <NA> <NA> association_only <NA> <NA>
#> 3 <NA> <NA> association_only <NA> <NA>
#> 4 <NA> <NA> association_only <NA> <NA>
#> 5 <NA> <NA> association_only <NA> <NA>
#> 6 <NA> <NA> association_only <NA> <NA>
#> compound_name_annotation.y hmdb_id_annotation.y kegg_id_annotation.y
#> 1 TRICARBALLYLATE HMDB0031193 C19806
#> 2 _3_7_DIMETHYLURATE HMDB0001982 C16360
#> 3 TRYPTOPHYLPROLINE HMDB0029091 <NA>
#> 4 PUTRESCINE HMDB0001414 C00134
#> 5 _1_METHYLXANTHINE HMDB0010738 <NA>
#> 6 _1_METHYLXANTHINE HMDB0010738 <NA>
#> annotation_level_annotation.y source_study_annotation.y
#> 1 high_confidence SINHA_CRC_2016
#> 2 high_confidence SINHA_CRC_2016
#> 3 high_confidence SINHA_CRC_2016
#> 4 high_confidence SINHA_CRC_2016
#> 5 high_confidence SINHA_CRC_2016
#> 6 high_confidence SINHA_CRC_2016
#> pathway_id_annotation.y pathway_name_annotation.y pathway_id_annotation
#> 1 <NA> <NA> <NA>
#> 2 <NA> <NA> <NA>
#> 3 <NA> <NA> <NA>
#> 4 <NA> <NA> <NA>
#> 5 <NA> <NA> <NA>
#> 6 <NA> <NA> <NA>
#> pathway_name_annotation reaction_id_annotation reaction_name_annotation
#> 1 <NA> <NA> <NA>
#> 2 <NA> <NA> <NA>
#> 3 <NA> <NA> <NA>
#> 4 <NA> <NA> <NA>
#> 5 <NA> <NA> <NA>
#> 6 <NA> <NA> <NA>
#> compound_name_annotation annotation_level_annotation mechanism_tier
#> 1 <NA> <NA> association_only
#> 2 <NA> <NA> association_only
#> 3 <NA> <NA> association_only
#> 4 <NA> <NA> association_only
#> 5 <NA> <NA> association_only
#> 6 <NA> <NA> association_only
#> mechanism_score
#> 1 0.5397279
#> 2 0.3145413
#> 3 0.2941110
#> 4 0.2847937
#> 5 0.2841477
#> 6 0.2730807