set.filter-methods: Setting filter to the analysis

Description Usage Arguments Details Value References Examples

Description

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

Usage

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## 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 [email protected].

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. [email protected] [x] ...

References

[x]

Examples

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# 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")

pievos101/PopGenome documentation built on Nov. 25, 2018, 10:26 p.m.