cistrans: Create and plot cis-trans map

In byandell/qtlview: Visualization of QTL Scans for Multiple Traits

Description

Creates cistrans object that can be plotted with different color schemes to accentuate strenght of LOD peak and proximity to physical location.

Usage

cistrans(x, filename, peak.chr, trans.chr, min.lod = 0,
  main, sep = "\t", use.density = TRUE, ...)
## S3 method for class 'cistrans'
plot(x, cex, main = attr(x, "main"),
  col.score = c("score","cis","trans"), cis.only,
  xlim, ylim, use.cM = FALSE, jitter = FALSE,
  peak.chr = attr(x, "peak.chr"), trans.chr = attr(x, "trans.chr"), ...)
## S3 method for class 'cistrans'
summary(object, ...)
## S3 method for class 'cistrans'
print(x, ...)

Arguments

x	data frame with LOD peak for traits (rows) and chromosomes (columns)
filename	name of file with x if it is to be read in
cross.name	name of cross (used by maps and trait.annotation)
maps	list of pull.map objects created by read.maps; default is associated with cross.name
peak.chr	names of chromosome(s) to show peaks
trans.chr	names of chromosome(s) to include traits
min.lod	minimum LOD to keep
main	title of plot (default taken from levels of x$Tissue
sep	separation character if reading in from filename
use.density	use density in plot of cumulative score if TRUE
trait.annotation	trait annotation data frame; default is associated with cross.name
use.annot	use annotation if TRUE
...	additional arguments passed to some subroutines

Details

The trait.annotation has a_gene_id column that is matched with x$a.gene.id to then use Chromosome and Chromosome_Position (in Mb) for plotting.

Value

Data frame of class cistrans with added components for summary and plot methods.

Author(s)

Brian S. Yandell

See Also

~~objects to See Also as help, ~~~

byandell/qtlview documentation built on May 13, 2019, 9:53 a.m.