qscore.summary {MANOR}R Documentation

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

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.

Value

A data.frame with 3 columns:

name qscore name
label qscore label
qscore quality qscore

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

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])

[Package MANOR version 1.4.0 Index]