maps: Create genetic and physical list of maps object.
In byandell/qtlview: Visualization of QTL Scans for Multiple Traits

Description Usage Arguments Details See Also Examples

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

read.maps(cross, filename, chr.valid, keep.nonseg = TRUE,
  drop.extra = TRUE, reset.chr = TRUE, interp.loc = TRUE,
  genotypes = c("A","H","B"), verbose = TRUE, ...)
## S3 method for class 'read.maps'
plot(x, main = "genetic vs. physical maps", ...)
## S3 method for class 'read.maps'
summary(object, ...)

`cross`	Objects of class `cross`. See `read.cross`.
`filename`	Name of file containing physical locations and detailed descriptions of markers.
`chr.valid`	Names of chromosomes to keep (default is all in `cross` object).
`keep.nonseg`	Keep non-segregating markers if `TRUE` (default). May be vector of marker names, or logical vector with names corresponding to markers.
`drop.extra`	Drop extra markers in `cross` object if not found in file when `TRUE` (default). If `FALSE`, then physical locations for extra markers will be interpolated.
`reset.chr`	Reset `chr` value for markers with missing values in physical location file using `cross` object if `TRUE` (default). If `FALSE`, markers with missing `chr` values are dropped.
`interp.loc`	Interpolate physical location if missing using `cross` object when `TRUE` (default).
`genotypes`	Genotype names to be used in plots and summaries.
`verbose`	Verbose listing if `TRUE` (default).
`x,object`	Object of class `read.maps`.
`main`	Main title for plot.
`...`	Arguments passed to `plot` or `summary` method.

Supplied by NCBI via Ron Zhu. The object created by this routine has both physical (Mb) and genetic (cM) distances along each chromosome. It can have markers that are part of map, as well as markers that are the same for parents (suggesting non-segregating regions of nearly same genotype).

Routine assumes physical location file has columns identified as snp = marker ID; chr = chromosome name (must match cross object); loc = physical location in Morgans; orient = orientation on chromosome (ignored for now).

snp.record

## Not run: 
## Keep only SNPs with decent records.
keep <- snp.record$Keep
names(keep) <- snp.record$Build36.SNP
## Create new maps object.
B6BTBR07.maps <-
  read.maps(B6BTBR07, "http://attie.wisc.edu/lab/data/data_for_intranet/snps/snp_4853.txt", keep = keep)

## End(Not run)