outlierFinder | R Documentation |
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.
outlierFinder(
similarity.mat,
bonf.prob = 0.05,
transFun = atanh,
normal.upper.thresh = NULL,
tail = "upper"
)
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. |
Returns either NULL or a dataframe with three columns: sample1, sample2, and similarity.
Levi Waldron, Markus Riester, Marcel Ramos
library(curatedOvarianData)
data(GSE32063_eset)
cormat <- cor(exprs(GSE32063_eset))
outlierFinder(cormat, bonf.prob = 0.05)
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