build_standard_table: Builds count tables using various mutation type schemas

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

Builds count tables using various mutation type schemas

Description

Generates count tables for different mutation type schemas which can be used as input to the mutational signature discovery or prediction functions. "SBS96" generates a table for single base substitutions following the standard 96 mutation types derived from the trinucleotide context. "SBS192" is the 96 mutation type schema with the addition of transcriptional strand or replication strand information added to each base. "DBS" generates a table for the double base substitution schema used in COSMIC V3. "Indel" generates a table for insertions and deletions following the schema used in COSMIC V3.

Usage

build_standard_table(
  musica,
  g,
  table_name,
  strand_type = NULL,
  overwrite = FALSE,
  verbose = FALSE
)

Arguments

musica	A musica object.
g	A BSgenome object indicating which genome reference the variants and their coordinates were derived from.
table_name	Name of standard table to build. One of "SBS96", "SBS192", "DBS", or "Indel".
strand_type	Strand type to use in SBS192 schema. One of "Transcript_Strand" or "Replication_Strand". Only used if table_name = SBS192.
overwrite	If TRUE, any existing count table with the same name will be overwritten. If FALSE, then an error will be thrown if a table with the same name exists within the musica object.
verbose	Show progress bar for processed samples

Value

No object will be returned. The count tables will be automatically added to the musica object.

Examples

g <- select_genome("19")

data(musica)
build_standard_table(musica, g, "SBS96", overwrite = TRUE)

data(musica)
annotate_transcript_strand(musica, "19")
build_standard_table(musica, g, "SBS192", "Transcript_Strand")

data(musica)
data(rep_range)
annotate_replication_strand(musica, rep_range)
build_standard_table(musica, g, "SBS192", "Replication_Strand")

data(dbs_musica)
build_standard_table(dbs_musica, g, "DBS", overwrite = TRUE)

data(indel_musica)
build_standard_table(indel_musica, g, table_name = "INDEL")

campbio/musicatk documentation built on July 14, 2024, 8:28 a.m.