qscore.summary: Compute quality scores for a given arrayCGH object
In MANOR: CGH Micro-Array NORmalization

Description Usage Arguments Details Value Note Author(s) See Also Examples

Compute useful quality scores for the arrayCGH and display them in a convenient way

1	qscore.summary.arrayCGH(arrayCGH, qscore.list)

`arrayCGH`	an object of type `arrayCGH`
`qscore.list`	a list of objects of type `qscore`

This function is used by the function html.report for the generation of an HMTL report of the normalization step. It can also be used by itself.

A data.frame with 3 columns:

`name`	qscore name
`label`	qscore label
`qscore`	quality qscore

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

Pierre Neuvial, manor@curie.fr.

qscore, qscore.summary, html.report

data(qscores)
data(spatial)

## define a list of qscores
qscore.list <- list(clone=clone.qscore, pct.clone=pct.clone.qscore,
pct.spot=pct.spot.qscore, pct.replicate=pct.replicate.qscore,
smoothness=smoothness.qscore, dyn.x=dyn.x.qscore, dyn.y=dyn.y.qscore,
var.replicate=var.replicate.qscore)

## compute quality scores for a couple of normalized arrays
gradient.norm$quality <- qscore.summary.arrayCGH(gradient.norm,
qscore.list)
print(gradient.norm$quality[, 2:3])

qscore.list$dyn.x$args$test <- 23
qscore.list$dyn.y$args$test <- 24
edge.norm$quality <- qscore.summary.arrayCGH(edge.norm, qscore.list)
print(edge.norm$quality[, 2:3])