Man pages for krisrs1128/phyloseqExtend
Extend Phyloseq to Rich Data Types

add_dim_namesAdd default row and column names for a spectra object
add_plot_layersHelper to add layers to ggplot plot
align_spectraWrapper for removeBaseline and alignSpectra in MALDIquant
filter_nonzeroVectorized filter function in the spirit of k over a
filter_varianceVectorized variance filtering
get_annotationHelper to get annotation list from a physeq object
get_authorsGet authorship data associated with a UniProt XML
get_citationGet citation data associated with a UniProt XML
get_commentGet comment data associated with a UniProt XML
get_db_refGet database data associated with a UniProt XML
get_geneGet gene data associated with a UniProt XML
get_organismGet organism data associated with a UniProt XML
get_peaks_listWrapper for MALDIquant detectPeaks
get_ppmGet ppm values associated with a spectra matrix
get_proteinGet protein data associated with a UniProt XML
get_sequenceGet sequence data associated with a UniProt XML
get_sourceGet source data associated with a UniProt XML
get_spectra_at_peaksExtract Spectra at Peak Positions
get_spectra_at_peaks_zerosExtract Spectra at Peak Positions, with zeros for non-peaks
get_uniprot_infoExtract information from UniProt Accession ID
interpolate_duplicatesInterpolate Duplicated Values
merge_ctable_optsMerge default contingency table processing options
merge_spectra_optsMerge default spectra processing options
phyloseqExtendAssemble several data objects into a phyloseqExtend object.
phyloseqExtend-classThe high-level extended phyloseq object, including new slot...
plot_raw_spectraPlot Raw Spectra Intensities Across All Indices
plot_spectraPlot Spectra Intensities
plot_spectra_peaksPlot only the Peaks in a spectra matrix
process_ctableWrapper for contingency table processing
process_spectraWrapper for processing spectra matrices
prune_samples-character-spectra-methodDefine a prune_samples methods for spectra class
remove_baselineWrapper for removeBaseline and alignSpectra in MALDIquant
remove_outlier_spectraRemove Outliers
row_varFast row variance
rpkg_from_rpkmCompute RPKGs from RPKMs
show-phyloseqExtend-methodPrint a phyloseqExtend object
spectraBuild or access an object of class spectra
spectra-classThe S4 class for storing metabolomic information
spectraOrNull-classspectra S4 class with placeholder
subsample_spectra_colsSubsample spectra and filter spectra to range based on column...
subset_samples_spectraSubset the samples of an object of class spectra
krisrs1128/phyloseqExtend documentation built on May 18, 2017, 11:46 p.m.