readthis package may be used to easily read the data from some popular mutation callers into R environment. readthis functions can be supplied not only with the single file paths, but also with lists of files or even paths to the directories with files to be loaded (and cevodata object is to store the data from many samples!)
readthis functions return tibbles or list of tibbles. These tibbles/ objects usually are instances of cevo_<software_name> S3 classes. cevomod implements methods that allow to add these types of data to the cevodata objects conveniently.
Arguments
- cd
object - data
Object read with readthis functions
- ...
Other arguments
- name
Name for the data
- verbose
Verbose?
Functions
add_data(): add_data() function takes cevodata as the first argument, so it is a preferred method for adding data in R pipelines.add_to_cevodata(): add_to_cevodata() is a generic with a set of methods for different classes ofdata. These methods are called by add_data() function.
Examples
# library(cevomod)
ascat_dir <- system.file("extdata", "ASCAT", package = "readthis")
ascat <- readthis::read_ascat_files(ascat_dir)
cd <- init_cevodata("Test dataset") |>
add_data(ascat)
#> Using 'ascat_purity' as default purity measure