html.report {MANOR} | R Documentation |
Create an HTML file with various illustrations of array normalization, including plots before and after normalization, and statistics about flagged spots and clones
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, intensity=NULL, light=FALSE, file.name="report", width=10, height=5, ...) html.report.default(spot.data, clone.data=NULL, flag.data=NULL, quality.data=NULL, ...)
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 |
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
In order
none
People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.
Pierre Neuvial, manor@curie.fr.