mapParams: Parameters for mapping mixture components to distinct copy...

Description Usage Arguments See Also Examples

View source: R/copynumber-models.R

Description

Parameters for mapping mixture components to distinct copy number states

Usage

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mapParams(threshold = 0.1, proportion.subjects = 0.5,
  outlier.variance.ratio = 5, max.homozygous = c(-1.5, -0.5),
  min.foldchange = 1.5)

Arguments

threshold

numeric value in [0, 0.5]. For a given observation (sample), mixture component probabilities > threshold and less than 1-threshold are combined.

proportion.subjects

numeric value in [0, 1]. Two components are combined if the fraction of subjects with component probabilities in the range [threshold, 1-threshold] exceeds this value.

outlier.variance.ratio

if the ratio of the component variance to the median variance of the other component exceeds the value of this argument, the component is considered to correspond to outliers.

max.homozygous

length-2 numeric vector of cutoffs used for establishing a homozygous deletion component. The first element is the cutoff for the mean log R ratios when there are 2 or more states. The second element is the cutoff for the mean log R ratio when there are 3 or more states.

min.foldchange

a length-one numeric vector. When there are 3 or more states, we compute the ratio of the distance between the means of the sorted components 1 and 2 (the 2 components with lowest means) and the distance between the means of components 2 and 3. If the ratio (i) exceeds the value specified by this parameter, (ii) there are 3 or more states, and (iii) the first component has a mean less than max_homozygous[2], we infer that the first component is a homozygous deletion.

See Also

mapComponents

Examples

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CNPBayes documentation built on May 2, 2018, 3:57 a.m.