README.md

In vsbuffalo/angsdr: angsdr

angsdr: load ANGSD data into R

This is a (very unofficial) minimal R package to load data from ANGSD into R. So far it just loads ANGSD's pestPG file into a GenomicRanges GRanges object (or, optionally a data.frame). Eventually, I'll probably add other convenience functions to work with ANGSD data.

Installation

Clone this repository:

$ git clone [e-mail]:vsbuffalo/angsdr.git

and install with:

$ R CMD INSTALL angsdr

Example

Data from a pestPG file can be loaded with:

library(angsdr)
d <- readPestPG("inst/extdata/test.pestPG")

The function overlapWidths can be used to annotate a ANGSD GRanges object with the proportion of a window that overlaps a feature, given by another GRanges object. For example:

library(rtracklayer)
gtf <- import("your_species.gtf")
coding <- gtf[gtf$source == "protein_coding"]
reduced_coding <- reduce(coding, ignore.strand=TRUE)
d$coding <- overlapWidths(d, reduced_coding)

Development

Please feel free to fork and participate in this package's development! If you'd like features added, open an issue on Github.

vsbuffalo/angsdr documentation built on May 3, 2019, 7:07 p.m.