Package index • enONE

All functions

ApplyNormalization(): Applies normalization on sequencing data

AssessNormalization(): Assessments of normalization performance

BetweenStatPlot(): Box-violin plot comparing values between groups

Counts() `Counts<-`(): Accessor for the "counts" slot of Enone object.

CreateGroupMatrix(): Create a matrix for RUVSeq

DotPlot(): Dot-plot with mean_sd bar

FilterLowExprGene(): Filter Low Expressed Genes

FindEnrichment(): Find enriched genes between enrich and input samples

GeneSelection(): Gene set selection

OutlierTest(): Outlier Test

PCA_Biplot(): Biplot of individuals and variables

PCAplot(): PCA plot from counts matrix

PS.Est.Depth(): Esimate sequencing depth

UseNormalization(): Apply specific normalization method

countReplicate(): Count numbers of each members

createEnone(): Enone object and constructor

.keepConsRows(): Keep Consistent Rows in Object

.mean_sd(): Statistics summary (mean and +/- sd)

.safe_grep(): Safe grep

edgeRDE(): Wrapper of edgeR procedure

enONE(): Normalization and assessment in one function

enRUVg(): Remove unwanted variation using control genes

enRUVs(): Remove unwanted variation using control genes within replicates

getEnrichment(): Accessor of enrichment results

getFactor(): Accessor of Enone normalization factors

getGeneSet(): Accessor of gene set

getMetrics(): Accessor of Enone metrics

listParameter() getParameter(): Accessor of Enone parameter

getScore(): Accessor of Enone score

listNormalization(): Accessor of normalization methods

normDESeq(): Perform DESeq normalization

normPossionSeq(): Perform PossionSeq normalization

normRUV(): Perform RUV normalization

normTC(): Perform total count normalization

normTMM(): Perform TMM normalization

normUQ(): Perform upper-quartile normalization

reduceRes(): Combine list of DE results

synEnrichment(): Enrichment level of synthetic RNA