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

Global functions
CountOrRatios Man page Source code
DNAbin2DNASet Source code
LDAeffectsize Source code
addtaxlevel Source code
alphasample-class Man page
as.data.frame.alphasample Man page Source code
as.data.frame.diffAnalysisClass Man page Source code
build_tree Man page
build_tree,DNAStringSet Man page
build_tree,DNAStringSet-method Man page
build_tree,DNAbin Man page
build_tree,DNAbin-method Man page
build_tree,character Man page
build_tree,character-method Man page
checkotu Source code
checksample Source code
clustplotClass-class Man page
contribution Source code
convert_to_treedata Man page Source code
data-hmp_aerobiosis_small Man page
data-kostic2012crc Man page
data-test_otu_data Man page
diffAnalysisClass-class Man page
diff_analysis Man page Source code
diff_analysis.data.frame Man page Source code
diff_analysis.phyloseq Man page Source code
diffclass Source code
diffsubclass Source code
drop_taxa Man page
drop_taxa,data.frame Man page
drop_taxa,data.frame-method Man page
drop_taxa,phyloseq Man page
drop_taxa,phyloseq-method Man page
duplicatedtaxcheck Source code
fillNAtax Source code
filltaxname Source code
generalizedFC Man page Source code
generalizedFC.default Man page Source code
generalizedFC.formula Man page Source code
geom_ord_ellipse Man page Source code
getMeanMedian Man page Source code
get_alltaxadf Man page
get_alltaxadf,data.frame Man page
get_alltaxadf,data.frame-method Man page
get_alltaxadf,phyloseq Man page
get_alltaxadf,phyloseq-method Man page
get_alphaindex Man page
get_alphaindex,data.frame Man page
get_alphaindex,data.frame-method Man page
get_alphaindex,integer Man page
get_alphaindex,integer-method Man page
get_alphaindex,matrix Man page
get_alphaindex,matrix-method Man page
get_alphaindex,numeric Man page
get_alphaindex,numeric-method Man page
get_alphaindex,phyloseq Man page
get_alphaindex,phyloseq-method Man page
get_clust Man page Source code
get_clust.default Man page Source code
get_clust.dist Man page Source code
get_clust.phyloseq Man page Source code
get_comparelist Source code
get_coord Man page Source code
get_coord.pcoa Man page Source code
get_coord.prcomp Man page Source code
get_dist Man page Source code
get_dist.default Man page Source code
get_dist.phyloseq Man page Source code
get_extend Source code
get_pca Man page Source code
get_pca.default Man page Source code
get_pca.phyloseq Man page Source code
get_pcoa Man page Source code
get_pcoa.default Man page Source code
get_pcoa.dist Man page Source code
get_pcoa.phyloseq Man page Source code
get_taxadf Man page Source code
get_taxadf.default Man page Source code
get_taxadf.phyloseq Man page Source code
get_upset Man page
get_upset,data.frame Man page
get_upset,data.frame-method Man page
get_upset,phyloseq Man page
get_upset,phyloseq-method Man page
get_varct Man page Source code
get_varct.pcasample Man page Source code
get_varct.pcoa Man page Source code
get_varct.prcomp Man page Source code
get_vennlist Man page Source code
get_vennlist.default Man page Source code
get_vennlist.phyloseq Man page Source code
getalltaxdf Source code
getannotlabel Source code
getanova Source code
getcall Source code
getcladedf Source code
getcladelabelposition Source code
getclass2sub Source code
getclasslevels Source code
getcompareclass Source code
getcompareres Source code
getcomparesubclass Source code
getconsistentfeatures Source code
getellipsemap Source code
getfactormap Source code
getgfcwilc Source code
getlabeldf Source code
getotudata Source code
getpvalue Man page Source code
getpvalue.QuadTypeIndependenceTest Man page Source code
getpvalue.ScalarIndependenceTest Man page Source code
getpvalue.glm Man page Source code
getpvalue.htest Man page Source code
getpvalue.lm Man page Source code
getpvalue.lme Man page Source code
getpvalue.negbin Man page Source code
getsample Source code
getsecondTRUEvar Source code
getsecondvarlist Source code
getvarlist Source code
ggbartax Man page Source code
ggbartax.default Man page Source code
ggbartax.phyloseq Man page Source code
ggbox Man page
ggbox,alphasample Man page
ggbox,alphasample-method Man page
ggbox,data.frame Man page
ggbox,data.frame-method Man page
ggclust Man page Source code
ggclust.clustplotClass Man page Source code
ggdiffclade Man page Source code
ggdiffclade.data.frame Man page Source code
ggdiffclade.diffAnalysisClass Man page Source code
ggdifftaxbar Man page Source code
ggdifftaxbar,diffAnalysisClass Man page
ggdifftaxbar,diffAnalysisClass-method Man page
ggdifftaxbar.featureMeanMedian Man page Source code
ggeffectsize Man page Source code
ggeffectsize.data.frame Man page Source code
ggeffectsize.diffAnalysisClass Man page
ggordpoint Man page Source code
ggordpoint.default Man page Source code
ggordpoint.pcasample Man page Source code
ggrarecurve Man page Source code
ggrarecurve.default Man page Source code
ggrarecurve.phyloseq Man page Source code
guess_rownames Source code
hmp_aerobiosis_small Man page
import_dada2 Man page Source code
import_qiime2 Man page Source code
kostic2012crc Man page
mappingtaxda Man page Source code
mapplyretrieveSeq Man page Source code
match.call.defaults Source code
multi.compare Man page Source code
ordplotClass-class Man page
pcasample-class Man page
pcoa-class Man page
prcomp-class Man page
read.featuretab Source code
read.qza Man page Source code
read.taxa Source code
removeconstant Source code
repduplicatedtaxcheck Source code
retrieveSeq Man page Source code
rfimportance Source code
samplealpha Source code
sampledflist Man page Source code
seedind Source code
setfactorlevels Source code
show,diffAnalysisClass-method Man page
splitData Man page Source code
splitStrtoList Man page Source code
stat_rare Man page Source code
test_otu_data Man page
theme_taxbar Man page Source code
tidyEffectSize Source code
transformdf Source code
varcorf Source code
xiangpin/MicrobitaProcess documentation built on Nov. 12, 2019, 12:43 p.m.