wrapper_multinom_dataprep: Wrapper for the preparation of mutation data for multinomial...

In MultinomialMutations/MultinomialMutations: Fast multinomial regression for large cancer mutation datasets

Description

This function is a wrapper for the function count_table_prep_multinom that prepares the mutation data for multinomial (and binomial) regression. This wrapper was used in our analysis in Bertl et al. (2007) (see References).

Usage

wrapper_multinom_dataprep(cv, m, impute, datafolder, datafile, impfolder,
  data_source)

Arguments

cv	integer. Which cross-validation piece should be handled?
m	integer. Number of multiple imputation replicates. 0 means no imputation.
impute	logical. Impute missing values or remove them?
datafolder	character. The data is read from the file paste0(datafolder, datafile, cv-1).
datafile	character.
impfolder	character. Folder where the imputed data should be saved.
data_source	character. Either "fredriksson" or "pcawg".

Details

The scripts that were used to run this function and that show all settings used in Bertl et al. (2007) are available in this package in the folder inst/Bertl_et_al_2017. The pre-processed data can be downloaded from figshare.

Value

There is no return value. The reformatted and imputed data is saved along with the number of missing values and total mutation count.

Author(s)

Johanna Bertl

References

Bertl, J.; Guo, Q.; Rasmussen, M. J.; Besenbacher, S; Nielsen, M. M.; Hornshøj, H.; Pedersen, J. S. & Hobolth, A. A Site Specific Model And Analysis Of The Neutral Somatic Mutation Rate In Whole-Genome Cancer Data. bioRxiv, 2017. doi: https://doi.org/10.1101/122879 http://www.biorxiv.org/content/early/2017/06/21/122879

See Also

count_table_prep_multinom, cancermutations

MultinomialMutations/MultinomialMutations documentation built on May 22, 2019, 4:39 p.m.