readPestPG: Read a pestPG file from ANGSD

In vsbuffalo/angsdr: angsdr

Description

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

Usage

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):

• Watterson's theta (theta_w)

• pairwise diversity (theta_pi)

• Fu and Li (theta_fuli)

• Fay's H (theta_fayh)

• L (theta_l)

As well as the follwing neutrality test statistics:

• Tajima's D (taj_d)

• Fu and Li F (fuli_f)

• Fu and Li's D (fuli_d)

• Fay's H (fay_h)

• Zeng's E (zeng_e)

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