famlod: MERLIN 'famlod' Object

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

Description

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

Usage

famlod(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 nonparametric analysis is specified using at least one of the options --npl or --pairs. These compute LOD scores using the Kong and Cox linear model designated in the 'analysis' column of the file by character strings containing 'ALL' and 'pairs', respectively. The 'plod' score is calculated using the best fitting overall model. The 'lod' score is maximized within each family (LOD)

For more information, see MERLIN's website: http://csg.sph.umich.edu/abecasis/merlin/index.html

Value

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

• famlod: data.frame with 5 columns (chr, pos, family, analysis, lod, plod)

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

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

Examples

famlod_chr9 <- famlod("merlin_9_famA.lod")
famlod_chr24 <- famlod(c("merlin_2_famA.lod", "merlin_4_famA.lod"))
famlod_all <- famlod(list.files(path = "merlin/", pattern = "lod$"))

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