informative: Find markers informative between sample groups

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Find markers informative between sample groups

Usage

informative(gty, between, ...)

Arguments

gty	a genotypes object
between	expression for grouping samples (see Details)
...	other parameters to be passed to consensus() (such as nas.allowed)

Details

A marker is defined to be "informative" if it is not monomorphic across a group of samples. In the context of a genetic cross (eg. an F2 intercross), an informative marker is one with a fixed difference between the two parental lines. This function generalizes that idea to more than two groups: a marker is informative if it has a fixed difference between any pair of groups, as defined in the between expression.

The expression between can be protected for evaluation in the environment of the sample metadata in attr(gty, "ped") (view it with samples(gty)) by wrapping it in .(). To group on more than one variable, provide multiple expressions in a list or separate them with commas like .(expr1, expr2). (This syntax will be familiar to users of the plyr package.)

Consensus genotypes are first computed within the groups defined by unique values of between, and then markers with fixed differences between any two groups are idenfitied.

Value

a named logical vector, of length equal to the number of rows in gty, indicating whether a marker is informative in the given samples

See Also

segregating, fixed.diffs

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.