rqcCycleAverageQualityPcaPlot: Biplot of PCA of per cycle read average quality
In Rqc: Quality Control Tool for High-Throughput Sequencing Data

Description Usage Arguments Value Functions Author(s) Examples

View source: R/rqcCycleAverageQualityPcaPlot.R

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

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rqcCycleAverageQualityPcaCalc(rqcResultSet)

rqcCycleAverageQualityPcaPlot(rqcResultSet)

rqcResultSet

list of RqcResultSet objects created by rqc and rqcQA functions.

Plot object from ggplot function.

rqcCycleAverageQualityPcaCalc: calculates necessary statistics

Welliton Souza

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)