readPestPG: Read a pestPG file from ANGSD

Description Usage Arguments Details

Description

This function reads a pestPG file from ANGSD into either a GRanges object or a plain data.frame.

Usage

1
readPestPG(file, asGRanges = TRUE, physical = FALSE, asDataFrame = FALSE)

Arguments

file

the pestPG-formatted file from ANGSD

asGRanges

logical indicating whether to return a GRanges object. If FALSE, will return a data.frame.

physical

logical value indicating whether to use the window as the range, or whether to use the physical region the analysis included (for GRanges output only).

asDataFrame

logical value indicating whether to use Bioconductor's DataFrame rather than a standard data.frame. Requires asGRanges=FALSE.

Details

readPestPG loads a pestPG file into R, as either a GRanges object (with asGRanges=TRUE) or as a data.frame (with asGRanges=FALSE). When a GRanges object is returned, the summary statistics will be stored as elementMetadata columns. Additionally, a column named numsites specifies the number of bases used by ANGSD in the calculation of the summary statistics.

ANGSD's pestPG file includes the following estimators of theta (metadata column names in paranthesis):

As well as the follwing neutrality test statistics:


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