extractCytosinesFromFASTA: Extract cytosine coordinates

In methimpute: Imputation-guided re-construction of complete methylomes from WGBS data

Description

Extract cytosine coordinates and context information from a FASTA file. Cytosines in ambiguous reference contexts are not reported.

Usage

extractCytosinesFromFASTA(file, contexts = c("CG", "CHG", "CHH"),
  anchor.C = NULL)

Arguments

file	A character with the file name.
contexts	The contexts that should be extracted. If the contexts are named, the returned object will use those names for the contexts.
anchor.C	A named vector with positions of the anchoring C in the contexts. This is necessary to distinguish contexts such as C*C*CG (anchor.C = 2) and *C*CCG (anchor.C = 1). Names must match the contexts. If unspecified, the first C within each context will be taken as anchor.

Value

A GRanges-class object with coordinates of extracted cytosines and meta-data column 'context'.

Examples

## Read a non-compressed FASTA files:
filepath <- system.file("extdata", "arabidopsis_sequence.fa.gz", package="methimpute")

## Only CG context
cytosines <- extractCytosinesFromFASTA(filepath, contexts = 'CG')
table(cytosines$context)

## Split CG context into subcontexts
cytosines <- extractCytosinesFromFASTA(filepath,
               contexts = c('DCG', 'CCG'),
               anchor.C = c(DCG=2, CCG=2))
table(cytosines$context)
               
## With contexts that differ only by anchor
cytosines <- extractCytosinesFromFASTA(filepath,
               contexts = c('DCG', 'CCG', 'CCG', 'CWG', 'CHH'),
               anchor.C = c(DCG=2, CCG=2, CCG=1, CWG=1, CHH=1))
table(cytosines$context)
               
## With named contexts
contexts <- c(CG='DCG', CG='CCG', CHG='CCG', CHG='CWG', CHH='CHH')
cytosines <- extractCytosinesFromFASTA(filepath,
               contexts = contexts,
               anchor.C = c(DCG=2, CCG=2, CCG=1, CWG=1, CHH=1))
table(cytosines$context)

methimpute documentation built on Nov. 8, 2020, 5:47 p.m.