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.
Clone this repository:
$ git clone git@github.com:vsbuffalo/angsdr.git
and install with:
$ R CMD INSTALL angsdr
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)
Please feel free to fork and participate in this package's development! If you'd like features added, open an issue on Github.