read.cross: Read QTL data

In villegar/MetaPipe: A High-Performance Computing Pipeline for QTL Mapping of Large Ionomic and Metabolomic Datasets

Read QTL data

Description

Read QTL data from two sources, one containing genotypes and another one phenotypes.

Usage

read.cross(geno, pheno, wdir = here::here(), quiet = TRUE, ...)

Arguments

geno	Data frame or string (filename) to file containing genotype data. For example a genetic map like father_riparia.
pheno	Data frame or string (filename) to file containing phenotype data. For example, output from assess_normality.
wdir	Working directory.
quiet	Boolean flag to hide status messages.
...	Arguments passed on to qtl::read.cross.

Value

Object of cross class for QTL mapping.

See Also

Other QTL mapping functions: qtl_perm_test(), qtl_scone()

Examples

data(father_riparia)
data(ionomics)
ionomics_rev <- MetaPipe::replace_missing(ionomics, 
                                          excluded_columns = c(1, 2),
                                          replace_na =  TRUE)

ionomics_normalised <- 
  MetaPipe::assess_normality(ionomics_rev,
                             excluded_columns = c(1, 2),
                             out_prefix = "ionomics",
                             transf_vals = c(2, exp(1)),
                             show_stats = FALSE)
x_data <- MetaPipe::read.cross(father_riparia, 
                               ionomics_normalised$norm,
                               genotypes = c("nn", "np", "--"))


# Clean up example outputs
MetaPipe:::tidy_up(c("HIST_", "ionomics_"))

villegar/MetaPipe documentation built on Nov. 22, 2022, 10:44 p.m.