QFeatures-missing-data: Managing missing data

Description Usage Arguments Value See Also Examples

Description

This manual page describes the handling of missing values in QFeatures objects. In the following functions, if object is of class QFeatures, and optional assay index or name i can be specified to define the assay (by name of index) on which to operate.

The following functions are currently available:

See the Processing vignette for examples.

Usage

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## S4 method for signature 'SummarizedExperiment,missing'
zeroIsNA(object, i)

## S4 method for signature 'QFeatures,integer'
zeroIsNA(object, i)

## S4 method for signature 'QFeatures,numeric'
zeroIsNA(object, i)

## S4 method for signature 'QFeatures,character'
zeroIsNA(object, i)

## S4 method for signature 'SummarizedExperiment,missing'
infIsNA(object, i)

## S4 method for signature 'QFeatures,integer'
infIsNA(object, i)

## S4 method for signature 'QFeatures,numeric'
infIsNA(object, i)

## S4 method for signature 'QFeatures,character'
infIsNA(object, i)

## S4 method for signature 'SummarizedExperiment,missing'
nNA(object, i)

## S4 method for signature 'QFeatures,integer'
nNA(object, i)

## S4 method for signature 'QFeatures,numeric'
nNA(object, i)

## S4 method for signature 'QFeatures,character'
nNA(object, i)

## S4 method for signature 'SummarizedExperiment'
filterNA(object, pNA = 0)

## S4 method for signature 'QFeatures'
filterNA(object, pNA = 0, i)

Arguments

object

An object of class QFeatures or SummarizedExperiment.

i

One or more indices or names of the assay(s) to be processed.

pNA

numeric(1) providing the maximim percentage of missing values per feature (row) that is acceptable. Feature with higher percentages are removed. If 0 (default), features that contain any number of NA values are dropped.

Value

An instance of the same class as object.

See Also

The impute() for QFeautres instances.

Examples

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se_na2

## Summary if missing values
nNA(ft_na, 1)

## Remove rows with missing values
assay(filterNA(ft_na, i = 1))

## Replace NAs by zero and back
ft_na <- impute(ft_na, i = 1, method = "zero")
assay(ft_na)
ft_na <- zeroIsNA(ft_na, 1)
assay(ft_na)

QFeatures documentation built on Nov. 8, 2020, 6:51 p.m.