defineSeqinfo: Use package data to define a Seqinfo object

In steveped/chipExtra: Additional functions for working with ChIP-Seq data

Use package data to define a Seqinfo object

Description

Use package data to define a Seqinfo object

Usage

defineSeqinfo(
  build = c("GRCh38", "GRCh37", "GRCm39", "GRCm38", "hg19", "hg38", "T2T-CHM13v2.0",
    "mm39", "mm10"),
  chr = TRUE,
  mito,
  ...
)

Arguments

build	The Genome build used
chr	logical(1) Include the prefix "chr"
mito	Specify M or MT to include the mitochondrial chromosome. Omitted by default
...	Not used

Details

This function will create a Seqinfo object from pre-defined data from the Genome Reference Consortium. Returned objects will always be restricted to assembled molecules only. Currently implemented genome builds represent the four most common builds for ChIP-Seq analysis

Value

A Seqinfo object

Examples

defineSeqinfo("GRCh37", TRUE)
defineSeqinfo("GRCh37", FALSE, "MT")

steveped/chipExtra documentation built on May 2, 2024, 12:11 p.m.