qtl.heatmap


    Data frame, containing the SNP names, chromosome an dbp locations in columns 1 through 3 and LOD scores for all phenotyped in the remaining columns.
  


    Additional arguments to be passed to plot.
  


  This function accepts LOD scores and SNP locations and plots a heatmap of the QTL.  Each QTL is scaled to between 0 and 1 and the QTL are hierarchically clustered.  A tile plot is then created with QTL colored from white (strong) to black (weak).  The motivation for this plot is to visualize QTL that may be coincident across different phenotypes.


 mapping 

 QTL 

 QTLRel 

DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.

Daniel Gatti

DOQTL

Genotyping and QTL Mapping in DO Mice

qtl.heatmap function

Data frame, containing the SNP names, chromosome an dbp locations in columns 1 through 3 and LOD scores for all phenotyped in the remaining columns.

Additional arguments to be passed to plot.

This function accepts LOD scores and SNP locations and plots a heatmap of the QTL.  Each QTL is scaled to between 0 and 1 and the QTL are hierarchically clustered.  A tile plot is then created with QTL colored from white (strong) to black (weak).  The motivation for this plot is to visualize QTL that may be coincident across different phenotypes.

qtl.heatmap: Plot a Heatmap of all QTL

Description

Usage

Arguments

Value

See Also

Examples