partbl: MERLIN 'partbl' Object

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

Description

Returns an S3 object of class partbl which is basically a compact version of MERLIN's fam_parametric.tbl files.

Usage

partbl(fname)

Arguments

fname

Character vector containing the parametric.tbl file name(s) output by MERLIN.

Details

MERLIN's --tabulate option is used to output convenient tables summarising linkage analysis results in two files per chromosome: chrA_parametric.tbl and chrA_nonparametric.tbl.

The parametric.tbl file will be output if MERLIN is run with the option --model genetic_model.txt. This uses the genetic model specified in the input file to calculate three statistics: a multipoint parametric LOD score ('lod' column), an estimate of the proportion of linked families at a given locus ('alpha' column), and the corresponding maximum heterogeneity LOD score ('hlod' column). For more information, see MERLIN's website: http://csg.sph.umich.edu/abecasis/merlin/index.html

Value

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

• partbl: data.frame with 6 columns (chr, pos, model, lod, alpha, hlod)

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

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

Examples

partbl_chr9 <- partbl("chr9-parametric.tbl")
partbl_chr24 <- partbl(c("chr2-parametric.tbl", "chr4-parametric.tbl"))
partbl_all <- partbl(list.files(path = "merlin/", pattern = "-parametric.tbl"))

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