runAlign: Align the single-molecule data

In rhondabacher/methylscaper: Visualization of Methylation Data

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,
  score_cutoff = 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.
score_cutoff	(optional) Used mostly for testing purposes.

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)

rhondabacher/methylscaper documentation built on Oct. 10, 2024, 8:18 a.m.