npartbl: MERLIN 'npartbl' Object

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

Description

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

Usage

npartbl(fname)

Arguments

fname

Character vector containing the nonparametric.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 nonparametric.tbl file will be output if MERLIN is run with at least one of the options --npl or --pairs. These compute a LOD score using the Kong and Cox linear model, which is found in the 'lod' column. The two options are designated in the 'analysis' column of the file by character strings containing 'ALL' and 'pairs', respectively.

If the --exp option is also specified, an additional LOD score is calculated using the Kong and Cox exponential mode. This is found in the 'exlod' column.

If the family consists of a single affected sibpair, the 'ALL' and 'pairs' statistics will be identical. The 'pairs' statistic also considers sharing within inbred individuals. For more information, see MERLIN's website: http://csg.sph.umich.edu/abecasis/merlin/index.html

Value

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

• npartbl: data.frame with 4 or 5* columns (chr, pos, analysis, lod, exlod*)

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

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

• merlin_options: character vector of length 3, indicating the options inferred to have been supplied to MERLIN for the nonparametric linkage analysis

Examples

npartbl_chr9 <- npartbl("chr9-nonparametric.tbl")
npartbl_chr24 <- npartbl(c("chr2-parametric.tbl", "chr4-nonparametric.tbl"))
npartbl_all <- npartbl(list.files(path = "merlin/", pattern = "-nonparametric.tbl"))

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