findGenesInterval: Find candidate genes for QTL.

In jtlovell/qtlTools: Data Processing and Plotting in Association with R/qtl

Description

findGenesInterval Use the mapping position (inferred) of each gene to find potential candidates under a QTL confidence interval

Usage

findGenesInterval(findGenecM.output = NULL, calcCis.output = NULL,
  qtlname = NULL, chr, lowposition, highposition, geneID, geneChr,
  geneBp, genecM)

Arguments

findGenecM.output	Output from findGenecM If supplied, geneID, geneChr, geneBp and genecM are ignored
calcCis.output	Output from calcCis. If supplied, chr, lowposition and highposition are ignored
qtlname	Identifier of each qtl
chr	QTL Chromosome
lowposition	Lower confidence interval bound (cM)
highposition	Upper confidence interval bound (cM)
geneID	The name of each gene
geneChr	The chromosome of each gene
geneBp	The basepair position of each gene (not currently in use)
genecM	The mapping position of each gene
...	Not currently in use.

Value

A named list where each element corresponds to a provided QTL confidence interval. Character vectors in each element display potential candidate genes for each QTL.

jtlovell/qtlTools documentation built on May 20, 2019, 3:14 a.m.