getSeqInfo: Retrieve sequence length and other information

In pmoulos/sitadela: An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

Retrieve sequence length and other information

Description

This function retrieves sequence (chromosome) length and other information for a set of reference sequences for a sitadela supported organism. If the organism is supported by the getChromInfoFromUCSC of the GenomeInfoDb package, then this function is used, otherwise, a directo download from the UCSC golden path takes place to retrieve the required data.

Usage

    getSeqInfo(org, asSeqinfo = FALSE)

Arguments

org	a supported organism to retrieve sequence (aka chromosome) information for. See also addAnnotation about supported organisms.
asSeqinfo	return a Seqinfo object or a data.frame.

Value

The function returns a Seqinfo or a data.frame with the a subset of a Seqinfo information. See also Seqinfo.

Author(s)

Panagiotis Moulos

Examples

require(GenomeInfoDb)
s <- getSeqInfo("mm10")

pmoulos/sitadela documentation built on May 19, 2024, 3:52 a.m.