isOutlier: Identify if a cell is an outlier based on a metric

Description Usage Arguments Value Examples

View source: R/qc.R

Description

Convenience function to determine which values for a metric are outliers based on median-absolute-deviation (MAD).

Usage

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isOutlier(metric, nmads = 5, type = c("both", "lower", "higher"),
  log = FALSE, subset = NULL, batch = NULL)

Arguments

metric

numeric or integer vector of values for a metric

nmads

scalar, number of median-absolute-deviations away from median required for a value to be called an outlier

type

character scalar, choice indicate whether outliers should be looked for at both tails (default: "both") or only at the lower end ("lower") or the higher end ("higher")

log

logical, should the values of the metric be transformed to the log10 scale before computing median-absolute-deviation for outlier detection?

subset

logical or integer vector, which subset of values should be used to calculate the median/MAD? If NULL, all values are used. Missing values will trigger a warning and will be automatically ignored.

batch

factor of length equal to metric, specifying the batch to which each observation belongs. A median/MAD is calculated for each batch, and outliers are then identified within each batch.

Value

a logical vector of the same length as the metric argument

Examples

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data("sc_example_counts")
data("sc_example_cell_info")
pd <- new("AnnotatedDataFrame", data=sc_example_cell_info)
rownames(pd) <- pd$Cell
example_sceset <- newSCESet(countData=sc_example_counts, phenoData=pd)
example_sceset <- calculateQCMetrics(example_sceset)

## with a set of feature controls defined
example_sceset <- calculateQCMetrics(example_sceset, feature_controls = 1:40)
isOutlier(example_sceset$total_counts, nmads = 3)

scater documentation built on May 31, 2017, 3:08 p.m.

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