Description Usage Arguments Details
This function reads a pestPG file from ANGSD into either a
GRanges
object or a plain
data.frame
.
1 | readPestPG(file, asGRanges = TRUE, physical = FALSE, asDataFrame = FALSE)
|
file |
the pestPG-formatted file from ANGSD |
asGRanges |
|
physical |
|
asDataFrame |
|
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
)
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