create_bagel: Creates a bagel object from a variant table
In campbio/BAGEL: Novel Mutational Signature Analysis

Description Usage Arguments Value Examples

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create_bagel(
  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,
  verbose = TRUE
)

`x`	Any object that can be coerced to a data.table including a matrix or data.frame.
`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 `"Chromosome"`.
`start_col`	The name of the column that contains the start position for each variant. Default `"Start_Position"`.
`end_col`	The name of the column that contains the end position for each variant. Default `"End_Position"`.
`ref_col`	The name of the column that contains the reference base(s) for each variant. Default `"Tumor_Seq_Allele1"`.
`alt_col`	The name of the column that contains the alternative base(s) for each variant. Default `"Tumor_Seq_Allele2"`.
`sample_col`	The name of the column that contains the sample id for each variant. Default `"Tumor_Sample_Barcode"`.
`extra_fields`	Which additional fields to extract and include in the bagel object. Default `NULL`.
`verbose`	Whether to print status messages during error checking. Default `TRUE`.

Returns a bagel object

maf_file <- system.file("testdata", "public_TCGA.LUSC.maf",
package = "BAGEL")
variants <- extract_variants_from_maf_file(maf_file)
g <- select_genome("38")
bagel <- create_bagel(x = variants, genome = g)