MANOR (version 1.44.0)

html.report: Generate an HTML report of array normalization

Description

Create an HTML file with various illustrations of array normalization, including plots before and after normalization, and statistics about flagged spots and clones

Usage

"html.report"(array.norm, array.nonorm=NULL, dir.out=".",
array.name=NULL, x="PosOrder", y=c("LogRatioNorm", "LogRatio"), chrLim=NULL,
ylim=NULL, zlim=NULL, clim=NULL, intensity=NULL, light=FALSE,
file.name="report", width=10, height=5, ...)
  "html.report"(spot.data, clone.data=NULL, flag.data=NULL, quality.data=NULL, ...)

Arguments

array.norm

an object of type arrayCGH after normalization step

array.nonorm

an optional object of type arrayCGH after a normalization step with no flags

spot.data

a data.frame containing spot-level informations (e.g. arrayCGH\$arrayValues)

clone.data

a data.frame containing clone-level informations (e.g. arrayCGH\$cloneValues)

flag.data

a data.frame containing information about flags, with fields char, label, arg, count as generated by function flag.summary

quality.data

a data.frame containing information about quality scores with fields name, label, score as generated by function qscore.summary

dir.out

absolute path of a directory where the file is generated (defaults to the current directory)

array.name

name or identifier of the array

x

a variable name from arrayCGH\$cloneValues giving the order position of the clones along the genome (defaults to 'PosOrder')

y

a vector of one or two variable names to be passed to report.plot

chrLim

an optional variable name from arrayCGH\$cloneValues giving the limits of each chromosome

ylim

a numeric vector of length 2 to be passed to report.plot: y axis range of the genomic profile display

clim

a numeric vector of length 2 to be passed to report.plot: color range of the genomic profile

zlim

a numeric vector of length 2 to be passed to report.plot: color range for array image display

intensity

an optional list with names c("M.var", "A.var", "pred.var", "span"). The first 3 items specify existing variable names from arrayCGH\$arrayValues that will be used to draw a MA-plot. The last item is the value of the loess 'span'

light

boolean value: if (light), only the core of the html file is generated; if (!light), a complete html file is generated

file.name

file name of the generated report (defaults to "report")

width

plot width, in inches

height

plot height, in inches

...

further arguments to be passed to report.plot

Value

Details

This function creates an HTML report file showing - the array image and the genome representation before normalization (if array.nonorm is provided) and after normalization, and optionally a MA-plot - a table with information about the number of flagged spots for each flag, and the number of remaining spots after normalization - a table with information about various quality criteria for the array

See Also

flag.summary, report.plot