## ----style, include=FALSE, results='hide'---------------------------------- BiocStyle::markdown() library(kableExtra) library(magrittr) library(SummarizedExperiment) ## ----installation, eval=FALSE---------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("evaluomeR") ## ----sample-input---------------------------------------------------------- library(evaluomeR) data("ontMetrics") data("rnaMetrics") data("bioMetrics") ## ----correlations-1, echo=TRUE--------------------------------------------- library(evaluomeR) data("rnaMetrics") correlationSE <- metricsCorrelations(rnaMetrics, margins = c(4,4,12,10)) # Access the correlation matrix via its first assay: # assay(correlationSE,1) ## ----stability-1, results='hide', echo=TRUE-------------------------------- stabilityData <- stability(rnaMetrics, k=2, bs = 100) ## ----stability-1-assay, results='hide', echo=TRUE, eval=FALSE-------------- # assay(stabilityData, 1) ## ----stability-1-table, results='asis', echo=FALSE------------------------- data <- assay(stabilityData, 1) kable(data) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) ## ----stabilityRange-1, results='hide', echo=TRUE--------------------------- stabilityRangeData = stabilityRange(rnaMetrics, k.range=c(2,4), bs = 100) ## ----quality-1, results='hide', eval=TRUE, echo=TRUE----------------------- qualityData = quality(rnaMetrics, k = 4) ## ----quality-1-assay, results='hide', eval=FALSE, echo=TRUE---------------- # assay(qualityData,1) ## ----quality-1-table, results='asis', echo=FALSE--------------------------- data <- assay(qualityData,1) kable(data) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>% scroll_box(width = "100%") ## ----quality-range-1, results='hide', eval=TRUE, echo=TRUE----------------- k.range = c(4,6) qualityRangeData = qualityRange(rnaMetrics, k.range) ## ----quality-range-2, eval=TRUE, echo=TRUE--------------------------------- diff(k.range)+1 length(qualityRangeData) ## ----quality-range-3, eval=FALSE, echo=TRUE-------------------------------- # k5Data = qualityRangeData$k_5 # k5Data = qualityRangeData[["k_5"]] # k5Data = getDataQualityRange(qualityRangeData, 5) # assay(k5Data, 1) ## ----quality-range-table, results='asis', echo=FALSE----------------------- data <- assay(qualityRangeData$k_5, 1) kable(data) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>% scroll_box(width = "100%", height = "150px") ## ----general-func-noplot, eval=FALSE, echo=TRUE---------------------------- # stabilityData <- stability(rnaMetrics, k=5, bs = 50, getImages = FALSE) ## ----sessionInfo, eval=TRUE------------------------------------------------ sessionInfo()