calc_asm: Calculate ASM Score
In DAMEfinder: Finds DAMEs - Differential Allelicly MEthylated regions

Description Usage Arguments Details Value Examples

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.

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

`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.

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.

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

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)