set.filter-methods: Setting filter to the analysis

In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description

A generic function to set filter regarding e.g missing data.

Usage

## S4 method for signature 'GENOME'
set.filter(object,
missing.freqs=TRUE,
minor.freqs=FALSE,
maf.lower.bound=0,
maf.upper.bound=1,
miss.lower.bound=0,
miss.upper.bound=1)

Arguments

object	An object of class "GENOME"
missing.freqs	Set filter for missing data
minor.freqs	Set filter for the MAF
maf.lower.bound	frequency of the MAF
maf.upper.bound	...
miss.lower.bound	frequency of the missing freq.
miss.upper.bound	...

Details

This function sets the slot region.data@included.

Value

Returned value is a modified object of class "GENOME"

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The following slots will be modified in the "GENOME" object
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	Slot	Reference	Description
1.	region.data@included	[x]	...

References

[x]

Examples

# GENOME.class <- readData("\home\Alignments")
# GENOME.class <- set.filter(GENOME.class, missing.freqs=TRUE,
# miss.lower.bound=0, miss.upper.bound=0.2)
# now apply any statistic to the filtered data set.
# GENOME.class <- calc.fixed.shared(GENOME.class, subsites="included")

PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.