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Last data update: 2014.03.03

R: Generate an HTML report of array normalization

html.report

R Documentation

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

  ## S3 method for class 'arrayCGH'
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, ...)

  ## Default S3 method:
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`

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

Value

none

Note

People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.

Author(s)

Pierre Neuvial, manor@curie.fr.