adjust_matrix {cola} | R Documentation

## Remove rows with low variance and impute missing values

### Description

Remove rows with low variance and impute missing values

### Usage

    adjust_matrix(m, sd_quantile = 0.05, max_na = 0.25, verbose = TRUE)

### Arguments

`m` | A numeric matrix.
`sd_quantile` | Cutoff of the quantile of standard deviation. Rows with standard deviation less than it are removed.
`max_na` | Maximum NA fraction in each row. Rows with NA fraction larger than it are removed.
`verbose` | Whether to print messages.

### Details

The function uses `impute.knn` to impute missing values, then uses `adjust_outlier` to adjust outliers and removes rows with low standard deviations.

### Value

A numeric matrix.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### Examples

    set.seed(123)
    m = matrix(rnorm(100), nrow = 10)
    m[sample(length(m), 5)] = NA
    m[1, ] = 0
    m
    m2 = adjust_matrix(m)
    m2

[Package cola version 1.8.1 Index]