generate_null_activity_score_distribution | R Documentation |
This function generates a null distribution of activity scores by performing random sampling of marker metabolites and calculating activity scores through network analysis.
generate_null_activity_score_distribution(
annotation_table_all,
feature_table_marker,
metabolite_database,
metabolic_network,
permutation_times = 20,
threads = 8,
adduct.table = NULL,
column = c("rp", "hilic"),
ms1.match.ppm = 25,
mz.ppm.thr = 400,
include_hidden_metabolites = FALSE
)
annotation_table_all |
A data frame containing all annotated metabolites. |
feature_table_marker |
A data frame containing marker features. |
metabolite_database |
A metabolite database object used for annotation. |
metabolic_network |
An 'igraph' object representing the metabolic network. |
permutation_times |
Integer; number of permutations to perform. Default is '20'. |
threads |
Integer; number of parallel threads to use. Default is '8'. |
adduct.table |
Optional data frame specifying possible adducts. Default is 'NULL'. |
column |
Character; chromatography column type. Options are '"rp"' or '"hilic"'. Default is '"rp"'. |
ms1.match.ppm |
Numeric; MS1 matching tolerance in ppm. Default is '25'. |
mz.ppm.thr |
Numeric; M/Z tolerance threshold in ppm. Default is '400'. |
Logical; whether to include hidden metabolites in the network analysis. Default is 'FALSE'. |
A list of numeric vectors representing null activity scores for each permutation.
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