TargetExperiment-buildReport: TargetExperiment auxiliar function.

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description

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.

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

Usage

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

## 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)

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

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)

Arguments

object	TargetExperiment class object.
attributeThres	Numeric indicating the intervals extreme values.
imageFile	Character indicating the name of the file that contains the plot that could be insert in the report.
file	Character indicating the name of the report.
n	amount of colors.
wb	A workbook object that will contain the report.

Value

Workbook object.

colours.

Note

see full example in TargetExperiment-class

Author(s)

Gabriela A. Merino [e-mail], Cristobal Fresno [e-mail], Yanina Murua [e-mail], Andrea S. Llera [e-mail] and Elmer A. Fernandez [e-mail]

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")

## Loading the TargetExperimentList object
data(ampliPanel, package="TarSeqQC")
colors<-ggplotColours(ampliPanel, n=5)
## Loading the TargetExperimentList object
data(TEList, package="TarSeqQC")
colors<-ggplotColours(TEList, n=5)

gamerino/TarSeqQC documentation built on Feb. 3, 2020, 9:19 p.m.