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preprocessGenome

Source: R/preprocessGenome.R
preprocessGenome.Rd

This function reads and preprocesses (optionally `bgzip`ped) FASTA file with reference sequences.

Usage

preprocessGenome(genome.file, nthreads = 1, verbose = TRUE)

Arguments

genome.file

reference (genomic) sequences file location string.

nthreads

non-negative integer for the number of additional HTSlib threads to be used during file decompression (default: 1).

verbose

boolean to report progress and timings (default: TRUE).

Value

list object containing preprocessed reference sequence data.

Details

The function loads and preprocesses reference (genomic) sequences, saving time when methylation calling needs to be performed on multiple BAM files. Currently, reading the data is done by means of HTSlib, therefore it is possible to speed up the loading by means of HTSlib decompression threads when FASTA file is compressed by `bgzip`.

This function is also called internally when file location is supplied as an input for callMethylation method.

`preprocessGenome` checks if index file is present, and if not, creates it automatically. It is possible and recommended to use compressed FASTA file as an input, but the file must be compressed by `bgzip` (part of samtools/HTSlib). When FASTA file is compressed, faster loading can be achieved using (typically one) additional HTSlib decompression thread.

During loading, both lowercase and uppercase ACGTN symbols are allowed and correctly recognised, however all the other symbols (e.g., extended IUPAC symbols, MRSVWYHKDB) within sequences are converted to N.

Please also note that for the purpose of methylation calling, the very same reference genome must be used for both alignment (when BAM is produced) and calling cytosine methylation by callMethylation method.

See also

callMethylation for methylation calling, and `epialleleR` vignettes for the description of usage and sample data.

Block compression/decompression utility bgzip.

Examples

  genome.file <- system.file("extdata", "test", "reference.fasta.gz", package="epialleleR")
  genome.data <- preprocessGenome(genome.file)
#> Reading reference genome file 
#> [0.001s]