html.report {MANOR} | 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.

### See Also

`flag.summary`, `report.plot`

[Package MANOR version 1.52.1 Index]