genomeplot: Creation of Genome Graph files

In nplplot: Plotting Linkage and Association Results

Creation of Genome Graph files

Description

The genomeplot function generates two formatted files, one containing “chromosome base” formatted genome data and the other containing marker-specific results with dbSNP SNP IDs for displaying genome-wide data sets in the UCSC genome browser.

Usage

genomeplot(gg.data)

Arguments

gg.data

a file containing chromosome, marker, physical position and scores.

Details

gg.data example:

Chromosome   Marker   Position   TRAIT_ALL   
         5   M1       0.000      0.670
         5   -        2.500      0.640
         5   M3       5.000      0.590
         5   -        6.500      0.600
         5   M2       8.000      0.610                   
         8   M4       0.000      0.670
         8   -        2.500      0.640
         8   M6       5.000      0.590
         8   -        6.500      0.600
         8   M5       8.000      0.610 

Two files are created, “GG.positons.all” for the “chromosome base” format, and “GG.markers.all” for the marker-names based format. When there are multiple scores in gg.data file, this results in matched pairs of files, one for each score, labelled with the score names, e.g. GG.positions.score1.all, and GG.markers.score1.all, GG.positions.score2.all and GG.markers.score2.all, and so on.

Value

TRUE or FALSE depending on whether runs successfully.

Examples

## Not run: genomeplot("GG.data.all")

nplplot documentation built on May 20, 2022, 1:07 a.m.