fampar: MERLIN 'fampar' Object

In bahlolab/linkrvis: Visualise Output from Genetic Linkage Analysis Tools

Description

Returns an S3 object of class fampar which is basically a compact version of MERLIN's fam.par files.

Usage

fampar(fname)

Arguments

fname

Character vector containing the fam.par file name(s) output by MERLIN.

Details

MERLIN's --perFamily option is used to output LOD scores for each family based on if parametric and/or nonparametric analyses have been specified.

The parametric analysis is specified using the option --model genetic_model.txt. For more information, see MERLIN's website: http://csg.sph.umich.edu/abecasis/merlin/index.html

Value

S3 object of class fampar, which is a list with:

• fampar: data.frame with 5 columns (chr, family, position, lod, model)

• max_lods: data.frame with 3 columns (chr, family, max_lod)

• n_markers: data.frame with 2 columns (chr, n)

Examples

fampar_chr9 <- fampar("merlin_9_famA.par")
fampar_chr24 <- fampar(c("merlin_2_famA.par", "merlin_4_famA.par"))
fampar_all <- fampar(list.files(path = "merlin/", pattern = "par$"))

bahlolab/linkrvis documentation built on May 11, 2019, 5:25 p.m.