PathoStat: PathoStat Statistical Microbiome Analysis Package
Version 1.2.0

The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.

Browse man pages Browse package API and functions Browse package files

AuthorSolaiappan Manimaran <manimaran_1975@hotmail.com>, Matthew Bendall <bendall@gwmail.gwu.edu>, Sandro Valenzuela Diaz <sandrolvalenzuelad@gmail.com>, Eduardo Castro <castronallar@gmail.com>, Tyler Faits <tfaits@gmail.com>, W. Evan Johnson <wej@bu.edu>
Bioconductor views GraphAndNetwork Metagenomics Microarray Microbiome PatternLogic PrincipalComponent RNASeq Sequencing Software Visualization
Date of publicationNone
MaintainerSolaiappan Manimaran <manimaran_1975@hotmail.com>
LicenseGPL (>= 2)
Version1.2.0
URL https://github.com/mani2012/PathoStat
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PathoStat")

Man pages

coreOTU: Compute Core OTUs for the given data matrix
coreOTUModule: Server function for Core OTU Module
coreOTUModuleUI: UI function for Core OTU Module
coreOTUNormalize: Compute Empirical Bayes OTU Normalized data
coreOTUQuantile: Compute coreOTU Quantile Normalized data
createPathoStat: Generates a PathoStat object from the PathoScope reports for...
findRAfromCount: Return the Relative Abundance (RA) data for the given count...
findTaxonLevel: Find the taxonomy for the given taxon id
findTaxonLevelData: Find the taxonomy level data for the given taxon level
findTaxonMat: Find the Taxonomy Information Matrix
findTaxonomy: Find the taxonomy for each taxon ids
formatTaxTable: Format taxonomy table for rendering
get_core: Select rows of OTU matrix that meet given detection and...
get_coremat: Create core OTU matrix containing number of OTUs detected at...
get_coremat_lineplot: Create line plot from core OTU matrix
getShinyInput: Getter function to get the shinyInput option
getShinyInputCombat: Getter function to get the shinyInputCombat option
getShinyInputOrig: Getter function to get the shinyInputOrig option
grepTid: Greps the tid from the given identifier string
loadPathoscopeReports: Loads all data from a set of PathoID reports. For each column...
loadPstat: Load the R data(.rda) file with pathostat object
log2CPM: Compute log2(counts per mil reads) and library size for each...
pathostat: Build PathoStat-class object from its phyloseq component.
PathoStat-class: PathoStat class to store PathoStat input data including...
plotConfRegion: Compute the confidence region for the given proportions
pstat_data: pathostat object generated from example pathoscope report...
readPathoscopeData: Reads the data from PathoScope reports and returns a list of...
runPathoStat: Statistical Microbiome Analysis on the pathostat input and...
savePstat: Save the pathostat object to R data(.rda) file
setShinyInput: Setter function to set the shinyInput option
setShinyInputCombat: Setter function to set the shinyInputCombat option
setShinyInputOrig: Setter function to set the shinyInputOrig option
sizeNormalize: Normalize the given data based on library size

Functions

PathoStat-class Man page
checkregion Source code
confinterval Source code
coreOTU Man page Source code
coreOTUModule Man page Source code
coreOTUModuleUI Man page Source code
coreOTUNormalize Man page Source code
coreOTUQuantile Man page Source code
createPathoStat Man page Source code
findRAfromCount Man page Source code
findSelectedTaxonId Source code
findTaxonLevel Man page Source code
findTaxonLevelData Man page Source code
findTaxonLevels Source code
findTaxonMat Man page Source code
findTaxonomy Man page Source code
formatTaxTable Man page Source code
getShinyInput Man page Source code
getShinyInputCombat Man page Source code
getShinyInputOrig Man page Source code
get_core Man page Source code
get_coremat Man page Source code
get_coremat_heatmap Source code
get_coremat_lineplot Man page Source code
grepTid Man page Source code
loadPathoscopeReports Man page Source code
loadPstat Man page Source code
log2CPM Man page Source code
logitcheckregion Source code
logitconfinterval Source code
pathostat Man page Source code
pathostat1 Man page
plotConfRegion Man page Source code
prop_hash Source code
proportion Source code
proportionc Source code
pstat Man page
pstat_data Man page
readPathoscopeData Man page Source code
runPathoStat Man page Source code
savePstat Man page Source code
setShinyInput Man page Source code
setShinyInputCombat Man page Source code
setShinyInputOrig Man page Source code
sizeNormalize Man page Source code
taxon_hash_update Source code

Files

DESCRIPTION
NAMESPACE
R
R/allClasses.R
R/confRegion.R
R/coreOTUModule.R
R/normalization.R
R/pathoStat.R
R/taxonomy.R
R/utils.R
README.md
build
build/vignette.rds
data
data/asthma_pstat_data.rda
data/pstat_data.rda
data/pstat_data_2_L1.rda
data/pstat_data_2_L2.rda
inst
inst/NEWS.Rd
inst/doc
inst/doc/PathoStatAdvanced.R
inst/doc/PathoStatAdvanced.Rmd
inst/doc/PathoStatAdvanced.html
inst/doc/PathoStatIntro.Rmd
inst/doc/PathoStatIntro.html
inst/doc/PathoStatUserManual.R
inst/doc/PathoStatUserManual.Rmd
inst/doc/PathoStatUserManual.pdf
inst/example
inst/example/data
inst/example/data/Sample_01_1-sam-report.tsv
inst/example/data/Sample_01_2-sam-report.tsv
inst/example/data/Sample_01_3-sam-report.tsv
inst/example/data/Sample_02_1-sam-report.tsv
inst/example/data/Sample_02_2-sam-report.tsv
inst/example/data/Sample_02_3-sam-report.tsv
inst/example/data/Sample_03_1-sam-report.tsv
inst/example/data/Sample_03_2-sam-report.tsv
inst/example/data/Sample_03_3-sam-report.tsv
inst/example/data/sample_data.tsv
inst/example/pathostat_pipeline.R
inst/reports
inst/reports/PathoStat.html
inst/reports/libs
inst/reports/libs/bootstrap
inst/reports/libs/bootstrap/css
inst/reports/libs/bootstrap/css/bootstrap-responsive.min.css
inst/reports/libs/bootstrap/css/bootstrap.min.css
inst/reports/libs/bootstrap/css/user.css
inst/reports/libs/bootstrap/javascript
inst/reports/libs/bootstrap/javascript/bootstrap.min.js
inst/reports/libs/bootstrap/javascript/jquery-1.10.1.min.js
inst/reports/libs/bootstrap/javascript/user.js
inst/reports/pathostat_report.Rmd
inst/shiny
inst/shiny/PathoStat
inst/shiny/PathoStat/server.R
inst/shiny/PathoStat/ui.R
man
man/PathoStat-class.Rd
man/coreOTU.Rd
man/coreOTUModule.Rd
man/coreOTUModuleUI.Rd
man/coreOTUNormalize.Rd
man/coreOTUQuantile.Rd
man/createPathoStat.Rd
man/findRAfromCount.Rd
man/findTaxonLevel.Rd
man/findTaxonLevelData.Rd
man/findTaxonMat.Rd
man/findTaxonomy.Rd
man/formatTaxTable.Rd
man/getShinyInput.Rd
man/getShinyInputCombat.Rd
man/getShinyInputOrig.Rd
man/get_core.Rd
man/get_coremat.Rd
man/get_coremat_lineplot.Rd
man/grepTid.Rd
man/loadPathoscopeReports.Rd
man/loadPstat.Rd
man/log2CPM.Rd
man/pathostat.Rd
man/plotConfRegion.Rd
man/pstat_data.Rd
man/readPathoscopeData.Rd
man/runPathoStat.Rd
man/savePstat.Rd
man/setShinyInput.Rd
man/setShinyInputCombat.Rd
man/setShinyInputOrig.Rd
man/sizeNormalize.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_PathoStat.R
vignettes
vignettes/PathoStatAdvanced.Rmd
vignettes/PathoStatIntro.Rmd
vignettes/PathoStatUserManual.Rmd
vignettes/img
vignettes/img/cr.png
vignettes/img/cu.png
vignettes/img/de_limma.png
vignettes/img/de_rp.png
vignettes/img/de_table.png
vignettes/img/di_ad.png
vignettes/img/di_bd.png
vignettes/img/di_bip.png
vignettes/img/di_coo.png
vignettes/img/di_et.png
vignettes/img/pca_ev.png
vignettes/img/pca_pca.png
vignettes/img/ra_ct.png
vignettes/img/ra_heat.png
vignettes/img/ra_ra.png
vignettes/img/ra_summary.png
vignettes/img/ra_taxlevel.png
vignettes/img/ts.png
PathoStat documentation built on May 20, 2017, 10:38 p.m.