R/standard_tables.R
build_standard_table.Rd
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.
build_standard_table( musica, g, table_name, strand_type = NULL, overwrite = FALSE, verbose = FALSE )
musica | A |
---|---|
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 |
strand_type | Strand type to use in SBS192 schema. One of
|
overwrite | If |
verbose | Show progress bar for processed samples |
No object will be returned. The count tables will be automatically
added to the musica
object.
g <- select_genome("19") data(musica) build_standard_table(musica, g, "SBS96", overwrite = TRUE) #> Building count table from SBS with SBS96 schema #> Warning: Overwriting counts table: SBS96 data(musica) annotate_transcript_strand(musica, "19") #> 403 genes were dropped because they have exons located on both strands #> of the same reference sequence or on more than one reference sequence, #> so cannot be represented by a single genomic range. #> Use 'single.strand.genes.only=FALSE' to get all the genes in a #> GRangesList object, or use suppressMessages() to suppress this message. build_standard_table(musica, g, "SBS192", "Transcript_Strand") #> Building count table from SBS and Transcript_Strand with SBS192 schema data(musica) data(rep_range) annotate_replication_strand(musica, rep_range) build_standard_table(musica, g, "SBS192", "Replication_Strand") #> Building count table from SBS and Replication_Strand with SBS192 schema data(dbs_musica) build_standard_table(dbs_musica, g, "DBS", overwrite = TRUE) #> Building count table from DBS with DBS78 schema #> Warning: Overwriting counts table: DBS78 data(indel_musica) build_standard_table(indel_musica, g, table_name = "INDEL") #> Building count table from INDELs with IND83 schema #> Warning: data length differs from size of matrix: [43990 != 83 x 5]