qscores {MANOR}R Documentation

Examples of qscore objects (quality scores) to apply to CGH arrays

Description

This data set provides qscore objects that can be applied to normalized arrayCGH objects in order to evaluate data quality after normalization.

Usage

data(qscores)

Format

The following qscore objects are provided:
clone.qscore number of clones
pct.clone.qscore percentage of clones
pct.spot.qscore percentage of spots
pct.replicate.qscore average percentage of replicates
smoothness.qscore signal smoothness
var.replicate.qscore
dyn.x.qscore signal dynamics on X chromosome
dyn.y.qscore signal dynamics on Y chromosome

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.

Source

Institut Curie, manor@curie.fr.

See Also

spatial, qscore.summary.arrayCGH, qscore

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]