rqcCycleAverageQualityPcaCalc {Rqc} | R Documentation

## 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

### Author(s)

Welliton Souza

### 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)

[Package Rqc version 1.16.2 Index]