## ----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, message=FALSE---------------------------------------------- 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, message=FALSE-------------------- stabilityData <- stability(rnaMetrics, k=2, bs = 100) ## ----stability-0-assay, echo=TRUE--------------------------------------------- stabilityData ## ----stability-1-assay, results='hide', echo=TRUE, eval=FALSE----------------- # assay(stabilityData, "stability_mean") ## ----stability-1-table, results='asis', echo=FALSE---------------------------- data <- assay(stabilityData, "stability_mean") kable(data) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) ## ----stabilityRange-1, results='hide', echo=TRUE, message=FALSE--------------- stabilityRangeData = stabilityRange(rnaMetrics, k.range=c(2,4), bs = 100) ## ----quality-1, results='hide', eval=TRUE, echo=TRUE, message=FALSE----------- 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, message=FALSE----- 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) ## ----getOptimalKValue, results='hide', eval=TRUE, echo=TRUE, message=FALSE---- stabilityData <- stabilityRange(data=ontMetrics, k.range=c(2,4), bs=20, getImages = FALSE, seed=100) qualityData <- qualityRange(data=ontMetrics, k.range=c(2,4), getImages = FALSE, seed=100) kOptTable <- getOptimalKValue(stabilityData, qualityData) ## ----getOptimalKValue-table, results='asis', echo=FALSE----------------------- data <- kOptTable kable(data) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>% scroll_box(width = "100%", height = "150px") ## ----getOptimalKValue-delimited, results='hide', eval=TRUE, echo=TRUE--------- kOptTable <- getOptimalKValue(stabilityData, qualityData, k.range=c(3,4)) ## ----getOptimalKValue-table-delimited, results='asis', echo=FALSE------------- data <- kOptTable kable(data) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>% scroll_box(width = "100%", height = "150px") ## ----plotMetricsMinMax, results='hide', eval=TRUE, echo=TRUE------------------ plotMetricsMinMax(ontMetrics) ## ----plotMetricsBoxplot, results='hide', eval=TRUE, echo=TRUE----------------- plotMetricsBoxplot(rnaMetrics) ## ----plotMetricsCluster, results='hide', eval=TRUE, echo=TRUE----------------- plotMetricsCluster(ontMetrics) ## ----plotMetricsViolin, results='hide', eval=TRUE, echo=TRUE------------------ plotMetricsViolin(rnaMetrics) ## ----sessionInfo, eval=TRUE--------------------------------------------------- sessionInfo()