perms: Create list of scanone perm objects.

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

Description

Use cross and file of physical locations to create a list of R/qtl map objects.

Usage

read.perms(cross, filenames, row.names = NULL, perms,
  method = "hk", model = "normal", ...)
## S3 method for class 'read.perms'
summary(object, ...)
## S3 method for class 'read.perms'
plot(x, ...)

Arguments

cross	Objects of class cross. See read.cross.
filenames	Character vector of file names containing permutations. Needs to have names from c("both","female","male"). Files should be CSV saved from call to scanone with a large value (e.g. 10000) of n.perm. Usually will have two columns labeled A and X for autosomes and X chromosome, resp.
row.names	Argument for read.csv. Should be NULL if CSV file saved without row names, otherwise set to 1.
perms	Named list of data frames containing permutations. Each element should be a dataframe or scanoneperm object from scanone. Names must be from c("both","female","male").
object,x	Object of class read.perms.
...	Arguments to pass to plot or summary method.

Details

This collects together permutations for male, female and both sexes combined to be used for high throughput QTL scans. The data frames by sex are coerced to scanoneperm format.

Examples

## Not run: 
example(B6BTBR07n.perms)

## End(Not run)

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