RTIGER (version 2.1.0)

generateObject: Load data

Description

Load data

Usage

generateObject(experimentDesign = NULL,nstates = 3, rigidity=NULL,
seqlengths = NULL, verbose = TRUE)

Value

RTIGER object

Arguments

experimentDesign

a data Frame that contains minimum a column with the files direction (name of the column files) and another with a shorter name to be used inside the function.

nstates

the number of states to be fitted in the model. A standard setting would use 3 states (Homozygous1, Heterozygous, and Homozygous2).

rigidity

an integer number specifying the rigidity parameter to be used.

seqlengths

a named vector with the chromosome lenghts of the organism that the user is working with.

verbose

logical value. Whether to print info messages.

Examples

data("ATseqlengths")
path = system.file("extdata",  package = "RTIGER")
files = list.files(path, full.names = TRUE)
nam = sapply(list.files(path ), function(x) unlist(strsplit(x, split = "[.]"))[1])
expDesign = data.frame(files = files, name = nam)
names(ATseqlengths) = paste0("Chr", 1:5)
myres = generateObject(experimentDesign = expDesign,
              seqlengths = ATseqlengths,
              rigidity = 10
)