qscore.summary {MANOR} | R Documentation |
Compute useful quality scores for the arrayCGH
and display them
in a convenient way
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])