qtl2 Genotype Probabilities

Description Usage Arguments Details Value Examples

Uses package feather to convert R object created in R/qtl2 for fast access.

1	feather_genoprob(genoprob, fbase, fdir = ".", verbose = TRUE)

`genoprob`	Object of class `"calc_genoprob"`. For details, see the R/qtl2 developer guide and `calc_genoprob`.
`fbase`	Base of filename for feather database.
`fdir`	Directory for feather database.
`verbose`	Show warning of feather creation if `TRUE` (default).

The genotype probabilities are stored in separate databases for each chromosome as tables of (indivduals*genotypes) x (positions) in directory feather. The dim, dimnames and is_x_chr elements of the object have information about the entire feather database. If a feather_genoprob object is a subset of another such object, the chr, ind, and mar contain information about what is in the subset. However, the feather databases are not altered in a subset, and can be restored by feather_genoprob_restore. The actual elements of a feather_genoprob object are only accessible to the user after a call to unclass; instead the usual access to elements of the object invoke subset.feather_genoprob.

A list containing the attributes of genoprob and the address for the created feather database. Components are:

dim - List of all dimensions of 3-D arrays.
dimnames - List of all dimension names of 3-D arrays.
is_x_chr - Vector of all is_x_chr attributes.
chr - Vector of (subset of) chromosome names for this object.
ind - Vector of (subset of) individual names for this object.
mar - Vector of (subset of) marker names for this object.
feather - Names of feather databases: A = autosome database, X = X chromosome database (if needed).

library(qtl2)
grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
map <- insert_pseudomarkers(grav2$gmap, step=1)
probs <- calc_genoprob(grav2, map, error_prob=0.002)
dir <- tempdir()
fprobs <- feather_genoprob(probs, "grav2", dir)