runAlign {methylscaper} | R Documentation

## Align the single-molecule data

### Description

Runs the preprocessing methods for single-molecule data.

### Usage

    runAlign(
      ref,
      fasta,
      fasta_subset = seq(1, length(fasta)),
      multicoreParam = NULL,
      updateProgress = NULL,
      log_file = NULL
    )

### Arguments

`ref` | A reference sequence to align the reads to.
`fasta` | A list of reads/sequences from a single-molecule experiment (e.g. MAPit)
`fasta_subset` | (optional) A vector of indices indicating which sequences to process if a subset should be used. Leave this blank if all sequences should be processed.
`multicoreParam` | (optional) A MulticoreParam object, used to align sequences in parallel.
`updateProgress` | (optional) Used to add a progress bar to the Shiny app. Should not be used otherwise.
`log_file` | (optional) String indicating where to save a log of the alignment process. If left NULL, no log is saved. We highly recommend saving a log file.

### Value

The output is a list containing the the matrices 'gch' and 'hcg. Each is a dataframe with reads/cells on the rows and each column is a base-pair. The matrix represents the methylation state for cell across all base pairs. The coding is as follows: -2: unmethylated GCH or HCG site -1: base pairs between two unmethylated GCH or HCG sites 0: base pairs between mismatching methylation states of two GCH or HCG sites 1: base pairs between two methylated GCH or HCG sites 2: methylated GCH or HCG site

### Examples

    data(reads_sm)
    data(ref_seq)
    example_alignedseq <- runAlign(fasta=reads_sm, ref = ref_seq[[1]], fasta_subset = 1:150)

[Package methylscaper version 1.2.0 Index]