check.pigengene.input {Pigengene} | R Documentation

## Quality check on the imput

### Description

Checks `Data` and `Labels` for `NA` values, row and column names, etc.

### Usage

      check.pigengene.input(Data, Labels, na.rm = FALSE, naTolerance=0.05)

### 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.
`Labels` | A (preferably named) vector containing the Labels (condition types) for `Data`. Names must agree with rows of `Data`.
`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, the whole column will be removed.
`naTolerance` | Upper threshold on the fraction of entries per gene that can be missing. Genes with a larger fraction of missing entries are ignored. For genes with smaller fraction of NA entries, the missing values are imputed from their average expression in the other samples. See `check.pigengene.input`.

### Value

A list of:

`Data` | The checked `Data` matrix, `NA` possibly removed and rows are ordered as names of `Labels`.
`Labels` | The checked vector of `Labels`

### Author(s)

Habil Zare

### See Also

`check.nas`, `one.step.pigengene`, `Pigengene-package`

### Examples

         data(aml)
         Labels <- c(rep("AML",nrow(aml)))
         names(Labels) <- rownames(aml)
         c1 <- check.pigengene.input(Data=aml, Labels=Labels,na.rm=TRUE)
         Data <- c1$Data
         Labels <- c1$Labels

[Package Pigengene version 1.12.0 Index]