hc.ord: Order traits by similarity of LOD scores

Description Usage Arguments Value Author(s) See Also Examples

Description

Traits are ordered using Hierarchical clustering of scanone output by similar positions of QTL. Can be used outside of imagelods function to order traits, if several imagelod() plots need to be made (eg. for number of traits > 100)

Usage

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hc.ord(lods, cluster = TRUE)

Arguments

lods

Scanone output with c("chr","pos") columns removed

cluster

Logical; if TRUE, order of columns is clustered, otherwise, order is same as input order.

Value

Integer vector of lodcolumn order

Author(s)

Brian Yandell and Aimee Teo Broman

See Also

plot.aug.scanone

Examples

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data(fake.f2expr)
fake.f2expr <- calc.genoprob(fake.f2expr)

scan.f2 <- scanone(fake.f2expr,pheno.col=1:100, method="hk")

hc.ord(scan.f2[-(1:2)],cluster=TRUE)

atbroman/neqtl documentation built on May 10, 2019, 2:08 p.m.