plotCVBoxes: Boxplots of CV for qPCR Ct values.

In HTqPCR: Automated analysis of high-throughput qPCR data

Description

Function that will calculate the coefficients of variation across selected qPCR data, and plot the results in a boxplot.

Usage

plotCVBoxes(q, cards = TRUE, xlab = "", ylab = "CV", col = brewer.pal(5, "Spectral"), main = NULL, stratify, ...)

Arguments

q	object of class qPCRset.
cards	vector, the numbers of the cards to plot. Defaults to TRUE = all cards.
xlab	character string, label for the x-axis.
ylab	character string, label for the y-axis.
col	vector of colours to use.
main	character string, plot title.
stratify	character, specifying what to stratify the Ct values by. NULL, the default means no stratification, "type" is the feature types of the qPCRset, and "class" the feature class.
...	any other arguments will be passed to the boxplot function.

Details

The CV is calculated across all the selected cards based on each well position, without taking possibly replicated genes on the cards into consideration. "type" and "class" are automatically extracted from the qPCRset using featureType and featureClass.

Value

A plot is created on the current graphics device. The CV values are returned invisibly.

Author(s)

Heidi Dvinge

See Also

boxplot

Examples

# Load example data
data(qPCRraw)
# Make plot with all samples or just a few
plotCVBoxes(qPCRraw)
plotCVBoxes(qPCRraw, cards=c(1,4))
plotCVBoxes(qPCRraw, stratify="class")
x <- plotCVBoxes(qPCRraw, stratify="type")
x[1:10]

Example output

Loading required package: Biobase
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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't connect to server'
     Gene1      Gene2      Gene3      Gene4      Gene5      Gene6      Gene7 
0.04977863 0.05444996 0.09937149 0.04133659 0.04066838 0.32899162 0.03677892 
     Gene8      Gene9     Gene10 
0.14416654 0.34848454 0.08398214 

HTqPCR documentation built on Nov. 8, 2020, 6:51 p.m.