selectRegions {bayesCGH} | R Documentation |
The 'selectRegions' function takes a 'ClassifySegList' object (or subset) and identifies those regions on the genome that show high likelihoods of high proportions of chromosomal gains or losses.
The 'selectAmpsDels' function simply selects those regions on the genome that have previously been classified as amplified or deleted.
selectRegions(seg, arrays, plot = FALSE, summarise = TRUE, prob.prop = 0.9, prop.greater.than = 0.2, group.name = "", ...) selectAmpsDels(seg, arrays, group.name = "")
seg |
Object of class ClassifySegList |
arrays |
Vector describing which arrays of 'seg' should be considered in region selection. |
plot |
Should the selected regions be plotted (plotProportions)? |
summarise |
Should the selected regions be summarised (see Details). |
prob.prop |
Threshold probability; see Details. |
prop.greater.than |
Threshold proportion; see Details. |
group.name |
Name for group of arrays selected in 'arrays'. |
... |
Additional arguments to be passed to plotProportions. |
This function takes a 'ClassifySegList' object (or subset) and identifies those regions on the genome that show high likelihoods of high proportions of chromosomal gains or losses. Specifically, given a threshold proportion 'prop.greater.than', empirical Bayes methods are applied to calculate the posterior probability that the proportion of chromosomal gains or losses exceeds this threshold for each probe on the arrays.
Probe selection is then made on the basis of those regions for which this posterior probability exceeds some probability threshold 'prob.prop'.
If 'summarise = TRUE' the selected probes are summarised into continuous regions (summariseRegions).
List containing:
data |
Description of data used. |
gains |
Probability for each probe that the proportion of samples with a chromosomal gain at that probe exceeds that given as 'prop.greater.than'. |
losses |
Probability for each probe that the proportion of samples with a chromosomal loss at that probe exceeds that given as 'prop.greater.than'. |
summary |
If 'summarise = TRUE', a summary of regions (and genes) that have a probability greater than 'prob.prop' of having a proportion of samples with a chromosomal gain or loss exceeding that of 'prop.greater.than'. |
Thomas Hardcastle
Hardcastle 2008