get_genome_annotation: Get Genome Annotation

In ShixiangWang/sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Get Genome Annotation

Description

Get Genome Annotation

Usage

get_genome_annotation(
  data_type = c("chr_size", "centro_loc", "cytobands", "transcript", "gene"),
  chrs = paste0("chr", c(1:22, "X", "Y")),
  genome_build = c("hg19", "hg38", "T2T", "mm10", "mm9", "ce11")
)

Arguments

data_type	'chr_size' for chromosome size, 'centro_loc' for location of centromeres, 'cytobands' for location of chromosome cytobands and 'transcript' for location of transcripts.
chrs	chromosomes start with 'chr'
genome_build	one of 'hg19', 'hg38'

Value

a data.frame containing annotation data

Examples

df1 <- get_genome_annotation()
df1

df2 <- get_genome_annotation(genome_build = "hg38")
df2

df3 <- get_genome_annotation(data_type = "centro_loc")
df3

df4 <- get_genome_annotation(data_type = "centro_loc", genome_build = "hg38")
df4

df5 <- get_genome_annotation(data_type = "cytobands")
df5

df6 <- get_genome_annotation(data_type = "cytobands", genome_build = "hg38")
df6

ShixiangWang/sigminer documentation built on March 16, 2024, 12:30 p.m.