MANOR (version 1.44.0)

qscore.summary: Compute quality scores for a given arrayCGH object

Description

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

Usage

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

Arguments

arrayCGH

an object of type arrayCGH

qscore.list

a list of objects of type qscore

Value

A data.frame with 3 columns:

name

qscore name

label

qscore label

qscore

quality qscore

Details

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.

See Also

qscore, qscore.summary, html.report

Examples

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])