## ---- include=FALSE, echo=FALSE----------------------------------------------- # date: "`r doc_date()`" # "`r pkg_ver('BiocStyle')`" # ## ---- echo=FALSE, results="hide", message=FALSE------------------------------- require(knitr) opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE) ## ----style, echo=FALSE, results='asis'---------------------------------------- BiocStyle::markdown() ## ---- echo=FALSE, fig.cap="Reproducible Signal matrix", out.width = '100%'---- knitr::include_graphics("Marr_schematic.png") ## ----load-lib, message=FALSE-------------------------------------------------- library(marr) ## ----data-1, message=FALSE, warning=FALSE------------------------------------- data("msprepCOPD") msprepCOPD ## ----Marr_output-------------------------------------------------------------- library(marr) Marr_output<- Marr(msprepCOPD, pSamplepairs = 0.75, pFeatures = 0.75, alpha=0.05) Marr_output ## Head of reproducible sample pairs per metabolite (feature) head(MarrFeatures(Marr_output)) ## Head of reproducible metabolites (features) per sample pair head(MarrSamplepairs(Marr_output)) ## Percent of reproducible sample pairs per metabolite (feature) ##greater than 75% MarrFeaturesfiltered(Marr_output) ## Percent of reproducible metabolites (features) per sample pair ## greater than 75% MarrSamplepairsfiltered(Marr_output) ## ----fig.cap="Distribution of reproducible metabolites", plot-Marr-Samplepairs---- MarrPlotSamplepairs(Marr_output) ## ----fig.cap="Distribution of reproducible sample pairs",plot-Marr-Metabolites---- MarrPlotFeatures(Marr_output) ## ----byFeatures--------------------------------------------------------------- ## Filtering the data by reproducible features MarrFilterData(Marr_output, by = "features") ## Filtering the data by reproducible sample pairs MarrFilterData(Marr_output, by = "samplePairs") ## Filtering the data by both features and sample pairs MarrFilterData(Marr_output, by = "both") ## ----session-info------------------------------------------------------------- sessionInfo()