readMeths {segmentSeq} | R Documentation

## A function for reading data from the YAMA methylation aligner (or similarly parsed data) from which to identify methylation loci and/or differentially methylated regions.

### Description

This function takes as input a set of files that describe the number of times a set of cytosines are observed to be methylated or unmethylated in some high-throughput sequencing data. It merges the data from these files into an object of '`alignmentMeth`' class which can then be further processed to identify methylation loci.

### Usage

    readMeths(files, dir = ".", libnames, replicates, nonconversion, chrs)

### Arguments

`files` | A character vector defining the file names of the alignment files to be read in.
`dir` | The directory in which the files are located.
`libnames` | A character vector giving the names of the samples to be read in.
`replicates` | A vector defining the replicate structure of the data. The ‘i’th and ‘j’th libraries are treated as replicates if and only if replicates[i] == replicates[j].
`nonconversion` | A numeric vector (all members should lie between 0 and 1) defining the non-conversion rate of each library. See `alignmentMeth-class` for details.
`chrs` | An (optional) character vector giving the names of the chromosomes to be read from the files. If ommitted, all chromosomes will be read in.

### Value

An object of class `alignmentMeth`.

### Author(s)

Thomas J. Hardcastle

### See Also

`alignmentMeth-class`.

### Examples

    datadir <- system.file("extdata", package = "segmentSeq")
    files <- c("short_18B_C24_C24_trim.fastq_CG_methCalls.gz",
    "short_Sample_17A_trimmed.fastq_CG_methCalls.gz",
    "short_13_C24_col_trim.fastq_CG_methCalls.gz",
    "short_Sample_28_trimmed.fastq_CG_methCalls.gz")

    mD <- readMeths(files = files, dir = datadir,
    libnames = c("A1", "A2", "B1", "B2"), replicates = c("A","A","B","B"),
    nonconversion = c(0.004777, 0.005903, 0.016514, 0.006134))

[Package segmentSeq version 2.28.0 Index]