doppelgangR (version 1.0.2)

outlierFinder: Identifies outliers in a similarity matrix.

Description

By default uses the Fisher z-transform for Pearson correlation (atanh), and identifies outliers as those above the quantile of a skew-t distribution with mean and standard deviation estimated from the z-transformed matrix. The quantile is calculated from the Bonferroni-corrected cumulative probability of the upper tail.

Usage

outlierFinder(similarity.mat, bonf.prob = 0.05, transFun = atanh,
    normal.upper.thresh = NULL, tail = "upper")

Arguments

similarity.mat

A matrix of similarities - larger values mean more similar.

bonf.prob

Bonferroni-corrected probability. A raw.prob is calculated by dividing this by the number of non-missing values in similarity.mat, and the rejection threshold is qnorm(1-raw.prob, mean, sd) where mean and sd are estimated from the transFun-transformed similarity.mat.

transFun

A function applied to the numeric values of similarity.mat, that should result in normally-distributed values.

normal.upper.thresh

Instead of specifying bonf.prob and transFun, an upper similarity threshold can be set, and values above this will be considered likely duplicates. If specified, this over-rides bonf.prob.

tail

"upper" to look for samples with very high similarity values, "lower" to look for very low values, or "both" to look for both.

Value

• Returns either NULL or a dataframe with three columns: sample1, sample2, and similarity.

Examples

library(curatedOvarianData)
data(GSE32063_eset)
cormat <- cor(exprs(GSE32063_eset))
outlierFinder(cormat, bonf.prob = 0.05)