PopGenome (version 2.7.5)

set.filter-methods: Setting filter to the analysis

Description

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

Usage

# S4 method for 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

...

Value

Returned value is a modified object of class "GENOME" --------------------------------------------------------- The following slots will be modified in the "GENOME" object ---------------------------------------------------------

	Slot	Reference	Description
1.	region.data@included	[x]	...

Details

This function sets the slot region.data@included.

References

[x]

Examples

# NOT RUN {
# 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")
# }