get.gc.content: Return a named vector of GC-content for each genomic region

In metaseqR: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

Description

Returns a named numeric vector (names are the genomic region names, e.g. genes) given a data frame which can be converted to a GRanges object (e.g. it has at least chromosome, start, end fields). This function works best when the input annotation data frame has been retrieved using one of the SQL queries generated from get.ucsc.query, used in get.ucsc.annotation.

Usage

    get.gc.content(ann, org)

Arguments

ann	a data frame which can be converted to a GRanges object, that means it has at least the chromosome, start, end fields. Preferably, the output of link{get.ucsc.annotation}.
org	one of metaseqR supported organisms.

Value

A named numeric vector.

Author(s)

Panagiotis Moulos

Examples

ann <- get.ucsc.annotation("mm9","gene","ucsc")
gc <- get.gc.content(ann,"mm9")

metaseqR documentation built on Nov. 8, 2020, 5:57 p.m.