Build excel report of the Target Experiment.

Description

addStatSummSheet adds the statistics summary sheet to the workbook that contains the Target Experiment Report.

buildReport builds an excel file containing some statistical results. These are computed to the selected attribute (e.g. 'coverage') along features (e.g. 'amplicon') and genes. If 'imageFile' is null, the graph generated calling the generic plot function will be used.

ggplotColours is a function to know what color is used when ggplot is called.

Usage

addStatSummSheet(object, wb, attributeThres = c(0, 1, 50, 200, 500, Inf),
    imageFile)

## S4 method for signature 'TargetExperiment'
addStatSummSheet(object, wb,
    attributeThres = c(0, 1, 50, 200, 500, Inf), imageFile)

buildReport(object, attributeThres = c(0, 1, 50, 200, 500, Inf),
    imageFile = NULL, file)

## S4 method for signature 'TargetExperiment'
buildReport(object, attributeThres = c(0, 1, 50,
    200, 500, Inf), imageFile = NULL, file = "Results.xlsx")

ggplotColours(object, n)

## S4 method for signature 'TargetExperiment'
ggplotColours(object, n)

Arguments

Value

Workbook object.

NULL.

colours

Note

see full example in TargetExperiment-class

Author(s)

Gabriela A. Merino gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar and Elmer A. Fernandez efernandez@bdmg.com.ar

See Also

TargetExperiment-class

Examples

## Loading the TargetExperiment object
data(ampliPanel,package="TarSeqQC")
# definition of the interval extreme values
attributeThres<-c(0,1,50,200,500, Inf)

## Building the XLSX report
imageFile<-system.file("extdata", "plot.pdf", package="TarSeqQC",
mustWork=TRUE)
buildReport(ampliPanel, attributeThres=attributeThres, imageFile=imageFile,
file="results.xlsx")

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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(TarSeqQC)
Loading required package: GenomicRanges
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: 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: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Loading required package: ggplot2
Loading required package: plyr

Attaching package: 'plyr'

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

    compact

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

    desc

The following object is masked from 'package:S4Vectors':

    rename

Loading required package: openxlsx
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TarSeqQC/TargetExperiment-buildReport.Rd_%03d_medium.png", width=480, height=480)
> ### Name: addStatSummSheet
> ### Title: Build excel report of the Target Experiment.
> ### Aliases: addStatSummSheet addStatSummSheet,TargetExperiment-method
> ###   addStatSummSheet-methods buildReport
> ###   buildReport,TargetExperiment-method buildReport-methods ggplotColours
> ###   ggplotColours,TargetExperiment-method ggplotColours-methods
> 
> ### ** Examples
> 
> ## Loading the TargetExperiment object
> data(ampliPanel,package="TarSeqQC")
> # definition of the interval extreme values
> attributeThres<-c(0,1,50,200,500, Inf)
> 
> ## Building the XLSX report
> imageFile<-system.file("extdata", "plot.pdf", package="TarSeqQC",
+ mustWork=TRUE)
> buildReport(ampliPanel, attributeThres=attributeThres, imageFile=imageFile,
+ file="results.xlsx")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>