retrieve_features_by_taxa: retrieve_features_by_taxa(FuncExpObj = NULL, assay_for_matrix...
In johnmcculloch/JAMS_BW: Just A Microbiology System
View source: R/retrieve_features_by_taxa.R
retrieve_features_by_taxa R Documentation
retrieve_features_by_taxa(FuncExpObj = NULL, assay_for_matrix = "BaseCounts", wantedfeatures = NULL, wantedsamples = NULL, asPPM = TRUE, PPM_normalize_to_bases_sequenced = FALSE, PPMthreshold = 0)
Description
Returns a long form data frame of stratification by taxa of the relative abundance or number of bases wanted of functional features in wanted samples, given allfeaturesbytaxa_matrix and allfeaturesbytaxa_index metadata present in a JAMS SummarizedExperiment functional object.
Usage
retrieve_features_by_taxa(
FuncExpObj = NULL,
assay_for_matrix = "BaseCounts",
wantedfeatures = NULL,
wantedsamples = NULL,
asPPM = TRUE,
PPM_normalize_to_bases_sequenced = FALSE,
PPMthreshold = 0
)
johnmcculloch/JAMS_BW documentation built on Jan. 6, 2025, 5:14 a.m.
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View source: R/retrieve_features_by_taxa.R
| retrieve_features_by_taxa | R Documentation |
retrieve_features_by_taxa(FuncExpObj = NULL, assay_for_matrix = "BaseCounts", wantedfeatures = NULL, wantedsamples = NULL, asPPM = TRUE, PPM_normalize_to_bases_sequenced = FALSE, PPMthreshold = 0)
Description
Returns a long form data frame of stratification by taxa of the relative abundance or number of bases wanted of functional features in wanted samples, given allfeaturesbytaxa_matrix and allfeaturesbytaxa_index metadata present in a JAMS SummarizedExperiment functional object.
Usage
retrieve_features_by_taxa(
FuncExpObj = NULL,
assay_for_matrix = "BaseCounts",
wantedfeatures = NULL,
wantedsamples = NULL,
asPPM = TRUE,
PPM_normalize_to_bases_sequenced = FALSE,
PPMthreshold = 0
)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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