bedplot: Creation of BED and BedGraph custom tracks

In nplplot: Plotting Linkage and Association Results

Creation of BED and BedGraph custom tracks

Description

Generates matched sets of files for linkage or association statistics along a chromosome for viewing in the UCSC genome browser from an input file containing a table of marker names, physical positions and one or more statistical scores.

Usage

 bedplot(bed.data)

Arguments

bed.data

File containing a table of marker names, physical position and scores.

Details

bed.data example:

Marker   Position   TRAIT_ALL   
M1       144255     0.670
-        144305     0.640
M3       144355     0.590
-        144378     0.600
M2       144400     0.610

Bedplot creates two types of files: a BED.* file containing a custom BED annotation track and a BedGraph.* file custom BedGraph annotation track. These files have the same suffix as the input bed.data file. When there are multiple scores in bed.data file, a matched pair of BedGraph track BED track files is created for each score, labelled with the score names, as well as the chromosome numbers, e.g. BedGraph.score1.* and BED.score1.*, BedGraph.score2.* and BED.score2.*, etc.

Value

TRUE or FALSE depending on whether runs successfully.

Examples

## Not run: bedplot("bed.data.05")

nplplot documentation built on May 29, 2024, 4:43 a.m.