check.nas {Pigengene} | R Documentation

## Removes `NA`s from a data matrix

### Description

Checks `Data` for `NA` values.

### Usage

      check.nas(Data, naTolerance=0.05, na.rm=TRUE)

### Arguments

`Data` | A matrix or data frame containing the expression data, with genes corresponding to columns and rows corresponding to samples. Rows and columns must be named.
`naTolerance` | A number in the 0-1 range. If the frequency of `NA`s in a column of `Data` is more than this threshold , then that column will be removed.
`na.rm` | If `TRUE`, `NA`s in the Data will be replaces with the average of the column, however, if the frequency of `NA`s in the column is too high (i.e., more than `naTolerance`), the whole column will be removed.

### Value

A list of:

`cleaned` | The cleaned data with no `NA` value. Rows are the same as `Data`, but some columns may be deleted.
`tooNaGenes` | A character vector of those genes (i.e., column names of `Data`) that had too many `NA`s, and therefore were removed.
`replacedNaNum` | The number of `NA` entries in the matrix that were replaced with the average of the corresponding column (gene).

### Author(s)

Habil Zare

### See Also

`check.pigengene.input`, `Pigengene-package`

### Examples

         data(aml)
         dim(aml)
         aml[1:410]<-NA
         c1 <- check.nas(Data=aml)
         dim(c1$cleaned)
         c1$tooNaGenes
         rm(aml)

[Package Pigengene version 1.12.0 Index]