data.access: Data summaries of dlcross and dlmap objects

In dlmap: Detection Localization Mapping for QTL

Description

Access the number of unique genotyped individuals; unique phenotyped individuals; and number of markers on each map chromosome

Usage

ngen(object, ...)

## S3 method for class 'dlmap'
ngen(object, ...)

## S3 method for class 'dlcross'
ngen(object, ...)

nphen(object, ...)

## S3 method for class 'dlmap'
nphen(object, ...)

## S3 method for class 'dlcross'
nphen(object, ...)

nmrk(object, ...)

## S3 method for class 'dlmap'
nmrk(object, ...)

## S3 method for class 'dlcross'
nmrk(object, ...)

Arguments

object	Object of type dlcross or dlmap
...	Additional arguments

Value

ngen returns the number of unique genotyped individuals. nphen returns the number of unique phenotyped individuals - generally greater than or equal to ngen because of replicates. nmrk returns a vector indicating the number of markers on each chromosome.

Author(s)

Emma Huang and Andrew George

References

Huang, BE and George, AW. 2009. Look before you leap: A new approach to QTL mapping. TAG 119:899-911

B. Emma Huang, Rohan Shah, Andrew W. George (2012). dlmap: An R Package for Mixed Model QTL and Association Analysis. Journal of Statistical Software 50(6): 1-22. URL http://www.jstatsoft.org/v50/i06/.

Examples

# load dataset
data(BSdat)
data(BSphe2)

## Not run: 
# convert data to dlmap format
dl.in1 <- dlcross(format="rqtl", genobj=BSdat, idname="ID", fixpos=1)

ngen(dl.in1)
nphen(dl.in1)
nmrk(dl.in1)

# convert data with separate phenotypic trait file
dl.in2 <- dlcross(format="rqtl", genobj=BSdat, pheobj=BSphe2, idname="ID", step=5)

ngen(dl.in2)
nphen(dl.in2)
nmrk(dl.in2)

## End(Not run)

dlmap documentation built on May 2, 2019, 2:45 a.m.