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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Rqc)
Loading required package: BiocParallel
Loading required package: ShortRead
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Rqc/rqcCycleAverageQualityPcaPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rqcCycleAverageQualityPcaCalc
> ### Title: Biplot of PCA of per cycle read average quality
> ### Aliases: rqcCycleAverageQualityPcaCalc rqcCycleAverageQualityPcaPlot
> ### Keywords: graphics qc
> 
> ### ** 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")
/home/ddbj/local/lib64/R/library/Rqc/extdata/Rqc.rda has been loaded.
> rqcCycleAverageQualityPcaPlot(rqcResultSet)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>