build_standard_table: Builds a standard table from user variants

In campbio/BAGEL: Novel Mutational Signature Analysis

Description

Builds a standard table from user variants

Usage

build_standard_table(bay, g, table_name, strand_type = NA, overwrite = FALSE)

Arguments

bay	Input samples
g	A BSgenome object indicating which genome reference the variants and their coordinates were derived from.
table_name	Name of standard table to build SBS96, SBS192, DBS, or Indel
strand_type	Only for SBS192 Transcript_Strand or Replication_Strand
overwrite	Overwrite existing count table

Value

None

Examples

g <- select_genome("19")

bay <- readRDS(system.file("testdata", "bagel.rds", package = "BAGEL"))
build_standard_table(bay, g, "SBS96", overwrite = TRUE)

bay <- readRDS(system.file("testdata", "bagel.rds", package = "BAGEL"))
annotate_transcript_strand(bay, "19")
build_standard_table(bay, g, "SBS192", "Transcript_Strand")

bay <- readRDS(system.file("testdata", "bagel.rds", package = "BAGEL"))
annotate_replication_strand(bay, BAGEL::rep_range)
build_standard_table(bay, g, "SBS192", "Replication_Strand")

bay <- readRDS(system.file("testdata", "dbs_bagel.rds",
package = "BAGEL"))
build_standard_table(bay, g, "DBS")

bay <- readRDS(system.file("testdata", "indel_bagel.rds", package = "BAGEL"))
build_standard_table(bay, g, table_name = "INDEL")

campbio/BAGEL documentation built on Oct. 6, 2020, 3:59 a.m.