Given an output variable from a
GO_analyse analysis and a set of valid
filters and thresholds, returns an identically formatted list keeping only the
rows of the score table passing all the filters.
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The output of the
Additional pairs of filter and threshold values in the format "filter=threshold". Filters must be valid names from colnames(result$GO).
It is highly recommended to filter out GO terms with very few genes (e.g. less than 5 genes), as the scoring function is biased for those GO terms (see UsersGuide).
|total_count, total:||Filter keeping only GO terms associated with at least the given count of genes in the annotations provided.|
|p.val, p, P:|| Filter keeping only the GO terms with P-value lower or equal
to the given cutoff (This filter is only applicable after the use of the
|namespace, namespace_1003:||Filter keeping only the GO terms of a given type. Valid values are "biological_process", "molecular_function", and "cellular_component". Abbreviations "BP", "MF", and "CC" are also accepted.|
|data_count, data:|| Filter keeping only GO terms associated with at
least the given count of genes, present in the
|ave_rank, rank:||Filter keeping only GO terms with an ave_rank value equal or lower than the given cutoff (average of the rank of all genes annotated to the GO term).|
|ave_score, score:||Filter keeping only GO terms with an ave_score value equal or higher than the given cutoff (average of the score of all genes annotated to the GO term) Scores are the mean decrease in Gini index for the random forest, or the F-value for the ANOVA approach.|
A list formatted identically to the
result object provided, with an
added or updated
filters.GO slot stating the filters and cutoffs
applied, and restricted to:
the gene ontologies passing the given filters and cutoff values.
the genes mapped to those remaining ontologies (i.e. all genes not associated with an ontology are discarded in the output object).
gene-mapping annotations related to the remaining gene ontologies.
It is possible to further filter a filter result object. Some warnings may
appear if the new filter cutoff conflict with the ones previously applied
(stored in the
filters.GO slot of the filtered object).
Example of conflicting filter values are:
'biological_process' a result object that was
previously filtered for
'molecular_function' (no more
'BP' terms are present in the first filtered object).
filtering for a
total_count of 5 or more a result object
previously filtered for a
total_count of 10 or more.
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# load the sample output data data(AlvMac_results.pVal) # have an overview of the result variable str(AlvMac_results.pVal) # filter for Biological Processes associated with 5+ genes and <=0.05 P-value filtered_results <- subset_scores( result=AlvMac_results.pVal, total_count=5, p.val=0.05, namespace="BP") # have an overview of the filtered result variable str(filtered_results)
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