read_tuples {DAMEfinder} | R Documentation

## Read in list of methtuple files

### Description

This function reads in a list of files obtained from the methtuple tool. It filters out tuples based on the set minimum coverage (min_cov) and the maximum allowed distance (maxGap) between two genomic positions in a tuple.

### Usage

    read_tuples(files, sampleNames, minCoverage = 2, maxGap = 20, verbose = TRUE)

### Arguments

`files` | List of methtuple files.
`sampleNames` | Names of files in the list.
`minCoverage` | The minimum coverage per tuple. Tuples with a coverage < minCoverage are filtered out. Default = 2.
`maxGap` | The maximum allowed distance between two positions in a tuple. Only distances that are <= maxGap are kept. Default = 150 base pairs.
`verbose` | If the function should be verbose.

### Value

A list of data frames, where each data frame corresponds to one file.

### 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'))

[Package DAMEfinder version 1.2.0 Index]