Man pages for xiangpin/MicrobitaProcess
an package for analysis, visualization and biomarker discovery of microbiome

alphasample-classalphasample class
as.data.frameget the table of diffAnalysisClass
build_treebuilding tree
clustplotClass-classclustplotClass class
convert_to_treedataconvert dataframe contained hierarchical relationship or...
CountOrRatioscaculate the count or relative abundance of replicate element...
data-hmp_aerobiosis_small(Data) Small subset of the HMP 16S dataset
data-kostic2012crc(Data) Genomic analysis identifies association of...
data-test_otu_data(Data) simulated dataset.
diff_analysisDifferential expression analysis
diffAnalysisClass-classdiffAnalysisClass class
drop_taxaDropping Species with Few abundance and Few Occurrences
generalizedFCgeneralized fold change
geom_ord_ellipseadd confidence ellipse to ordinary plot
get_alltaxadfget the table of abundance of all level taxonomy
get_alphaindexalpha index
get_clustHierarchical cluster analysis for the samples
get_coordget ordination coordinates.
get_distcalculate distance
getMeanMedianget the mean and median of specific feature.
get_pcaPerforms a principal components analysis
get_pcoaperforms principal coordinate analysis (PCoA)
getpvalueMethods for computation of the p-value
get_taxadfget the data of specified taxonomy
get_upsetgenerate the dataset for upset of UpSetR
get_varctget the contribution of variables
get_vennlistgenerate a vennlist for VennDiagram
ggbartaxtaxonomy barplot
ggboxA box or violin plot with significance test
ggclustplot the result of hierarchical cluster analysis for the...
ggdiffcladeplot the clade tree with highlight
ggdifftaxbarsignificantly discriminative feature barplot
ggeffectsizevisualization of effect size by the Linear Discriminant...
ggordpointordination plotter based on ggplot2.
ggrarecurveRarefaction alpha index
import_dada2Import function to load the feature table and taxanomy table...
import_qiime2Import function to load the output of qiime2.
mappingtaxdagenerate the mapping data
mapplyretrieveSeqRetriveing Sequencing from NCBI By mapply
multi.comparea container for performing two or more sample test.
ordplotClass-classordplotClass class
pcasample-classpcasample class
pcoa-classpcoa class
prcomp-classprcomp class
read.qzaread the qza file, output of qiime2.
retrieveSeqRetriveing Sequencing from NCBI
sampledflistGenerate random data list from a original data.
show-methodsmethod extensions to show for diffAnalysisClass objects.
splitDataSplit Large Vector or DataFrame
splitStrtoListsplit a dataframe contained one column
stat_raremapping data of ggrarecurve
theme_taxbartheme_taxbar
xiangpin/MicrobitaProcess documentation built on Nov. 12, 2019, 12:43 p.m.