Creates a musica object from a variant table — create

This function creates a musica object from a variant table or matrix. The musica class stores variants information, variant-level annotations, sample-level annotations, and count tables and is used as input to the mutational signature discovery and prediction algorithms. The input variant table or matrix must have columns for chromosome, start position, end position, reference allele, alternate allele, and sample names. The column names in the variant table can be mapped using the chromosome_col, start_col, end_col, ref_col, alt_col, and sample_col parameters.

create_musica(
  x,
  genome,
  check_ref_chromosomes = TRUE,
  check_ref_bases = TRUE,
  chromosome_col = "chr",
  start_col = "start",
  end_col = "end",
  ref_col = "ref",
  alt_col = "alt",
  sample_col = "sample",
  extra_fields = NULL,
  standardize_indels = TRUE,
  convert_dbs = TRUE,
  verbose = TRUE
)

Arguments

x	A data.table, matrix, or data.frame that contains columns with the variant information.
genome	A BSgenome object indicating which genome reference the variants and their coordinates were derived from.
check_ref_chromosomes	Whether to peform a check to ensure that the chromosomes in the `variant` object match the reference chromosomes in the `genome` object. If there are mismatches, this may cause errors in downstream generation of count tables. If mismatches occur, an attept to be automatically fix these with the `seqlevelsStyle` function will be made. Default `TRUE`.
check_ref_bases	Whether to check if the reference bases in the `variant` object match the reference bases in the `genome` object. Default `TRUE`.
chromosome_col	The name of the column that contains the chromosome reference for each variant. Default `"chr"`.
start_col	The name of the column that contains the start position for each variant. Default `"start"`.
end_col	The name of the column that contains the end position for each variant. Default `"end"`.
ref_col	The name of the column that contains the reference base(s) for each variant. Default `"ref"`.
alt_col	The name of the column that contains the alternative base(s) for each variant. Default `"alt"`.
sample_col	The name of the column that contains the sample id for each variant. Default `"sample"`.
extra_fields	Which additional fields to extract and include in the musica object. Default `NULL`.
standardize_indels	Flag to convert indel style (e.g. `C > CAT` becomes `- > AT` and `GCACA > G` becomes `CACA > -`)
convert_dbs	Flag to convert adjacent SBS into DBS (original SBS are removed)
verbose	Whether to print status messages during error checking. Default `TRUE`.

Value

Returns a musica object

Examples

maf_file <- system.file("extdata", "public_TCGA.LUSC.maf",
package = "musicatk")
variants <- extract_variants_from_maf_file(maf_file)
g <- select_genome("38")
musica <- create_musica(x = variants, genome = g)
#> Checking that chromosomes in the 'variant' object match chromosomes in the 'genome' object.
#> Checking that the reference bases in the 'variant' object match the reference bases in the 'genome' object.
#> Standardizing INS/DEL style
#> Converting adjacent SBS into DBS
#> 4 SBS converted to DBS