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

  html.report.arrayCGH(array.norm, array.nonorm=NULL, dir.out=".",
array.name=NULL, x="PosOrder", y=c("LogRatioNorm", "LogRatio"), chrLim=NULL,
ylim=NULL, zlim=NULL, clim=NULL, light=FALSE, file.name="report",
width=10, height=5, ...) 
  html.report.default(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
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 - 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

Examples






[Package MANOR version 1.4.0 Index]