Rqc (version 1.6.2)

rqcCycleAverageQualityPcaCalc: Biplot of PCA of per cycle read average quality

Description

This function creates a Biplot of PCA of per cycle read average quality

Usage

rqcCycleAverageQualityPcaCalc(rqcResultSet)
rqcCycleAverageQualityPcaPlot(rqcResultSet)

Arguments

rqcResultSet

list of RqcResultSet objects created by rqc and rqcQA functions.

Value

Plot object from ggplot function.

Functions

• rqcCycleAverageQualityPcaCalc: calculates necessary statistics

Examples

checkpoint("Rqc", path=system.file(package="Rqc", "extdata"), {
  folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147")
  files <- list.files(full.names=TRUE, path=folder)
  rqcResultSet <- rqcQA(files, pair=c(1,1), workers=1)
}, keep="rqcResultSet")
rqcCycleAverageQualityPcaPlot(rqcResultSet)