calc_asm {DAMEfinder} | R Documentation

## Calculate ASM Score

### Description

This function takes in a list of samples resulting from the read_tuples function and returns a SummarizedExperiment of Allele-Specific Methylation (ASM) scores, where each row is a tuple and each column is a sample.

### Usage

    calc_asm(
      sampleList,
      beta = 0.5,
      a = 0.2,
      transform = modulus_sqrt,
      coverage = 5,
      verbose = TRUE
    )

### Arguments

`sampleList` | List of samples returned from `read_tuples`
`beta` | The beta parameter used to calculate the weight in the ASM score. `link{calc_weight}` uses this parameter to penalize fully methylated or unmethylated tuples. Default = 0.5.
`a` | The distance from 0.5 allowed, where 0.5 is a perfect MM:UU balance for a tuple. In the default mode this value is set to 0.2, and we account for the instances where the balance is between 0.3 and 0.7.
`transform` | Transform the calculated tuple ASM scores. We use the modulus square root function which outputs the square root, while preserving the original sign.
`coverage` | Remove tuples with total reads below coverage. Default = 5.
`verbose` | If the function should be verbose. Default = TRUE.

### Details

Calculates ASM score for a list of samples in the output format of the result of read_tuples This functions uses the following other functions: process, calcScore, calcWeight.

### Value

A `SummarizedExperiment` of ASM scores where the rows are all the tuples and the columns the sample names.

### Examples

    DATA_PATH_DIR <- system.file('extdata', '.', package = 'DAMEfinder')
    get_data_path <- function(file_name) file.path(DATA_PATH_DIR, file_name)

    tuple_files <- list.files(DATA_PATH_DIR, '.tsv.gz')
    tuple_files <- get_data_path(tuple_files)
    ASM <- read_tuples(tuple_files, c('CRC1', 'NORM1'))
    ASMscore <- calc_asm(ASM)

[Package DAMEfinder version 1.2.0 Index]