cluster_qtl: Group QTL from different experiments into blocks.

In ellisztamas/arghqtl: Tools for plotting and downstream analysis of R/QTL objects in R

Description

Loci in a list of QTL objects are grouped by position. Loci are declared to be colocalised if the confidence intervals on locus position overlap. When the position of a QTL is poorly defined and confidence intervals are large, the locus colocalises with many other loci, probably erroneously. To combat this, set a maximum length using the argument threshold; QTL with confidence intervals longer than this will be excluded from clustering.

Usage

cluster_qtl(
  chr,
  qtl_list,
  model_fit_list,
  threshold = NULL,
  hard_boundary = TRUE,
  qtl_labels = "QTL"
)

Arguments

chr	A numeric vector listing which chromosomes are to be plotted.
qtl_list	A list of QTL objects from r/qtl (i.e list(object1, object2, ...)).
model_fit_list	A list of model fit objects (i.e. objects outputted from 'fit.qtl').
threshold	Maximum length in centimorgans above which QTL are considered to be poorly defined and excluded from clustering.
hard_boundary	Logical. Determines whether to separate pairs QTL that overlap at only a single marker, i.e. the end of the credible interval of the first QTL falls at the same marker where the credible interval begins. If TRUE, these QTL are treated as distinct. Defaults to TRUE.
qtl_labels	Prefix for labels for QTL. Usually a string. Defaults to "QTL".

Value

Two data frames:

1. 1. A summary table of each cluster, indicating the mean and the maximum extent of 95 percentage of total phenotypic variance explained for all QTL in the cluster. See ?cluster_qtl_summary.

2. 2. Full details of all the QTL, indicating which clutser they belong to.

ellisztamas/arghqtl documentation built on March 18, 2021, 9:44 p.m.