normalize_counts {mpra} | R Documentation

## Total count normalization of DNA and RNA counts

### Description

Total count normalization of DNA and RNA counts.

### Usage

    normalize_counts(object, block = NULL)

### Arguments

`object` | An object of class `MPRASet`.
`block` | A vector giving the sample designations of the columns of `object`. The default, `NULL`, indicates that all columns are separate samples.

### Details

`block` is a vector that is used when the columns of the `MPRAset` object are paired. This often is the case when comparing allelic versions of an element. In this case, the first $s$ columns of `object` give the counts for the reference allele in $s$ samples. The second $s$ columns give the counts for the alternative allele measured in the same $s$ samples. With 3 samples, `block` would be `c(1,2,3,1,2,3)`. All columns are scaled to have 10 million counts.

### Value

An object of class `MPRASet` with the total count-normalized DNA and RNA counts.

### Examples

    data(mpraSetAggExample)
    mpraSetAggExample <- normalize_counts(mpraSetAggExample)

[Package mpra version 1.12.1 Index]