univariate_cox_model: This function performs survival analysis for mutation counts...

In ginnyintifa/GPD:

Description

This function performs survival analysis for mutation counts mapped to PIU, LU and NCU.

Usage

univariate_cox_model(piu_filename, lu_filename, ncu_filename, clinical_df,
  gender_as_covariate = T, race_group_min = 6, min_surv_days = 90,
  min_surv_people = 5, patient_sum_min = 3,
  mutation_type = "somatic", output_dir)

Arguments

piu_filename	Filename for the PIU mapping results.
lu_filename	Filename for the LU mapping results.
ncu_filename	Filename for the NCU mapping results.
clinical_df	Clinical information data frame.
gender_as_covariate	Boolean variable indicating gender should be taken as a covariable.
race_group_min	The minimum number of patients with the same race enough for a race group.
min_surv_days	The minimum number of survival time (in days) a patient has to be included in analysis.
min_surv_people	The minimum number of patients survived (or censored) in a cohort that a survival analysis should be conducted.
patient_sum_min	The minimum number of patients having mutation mapping to the unit for the unit to be analysed.
mutation_type	A tag indicating the type of mutation; somatic or germline.
output_dir	The directory you would like to have your output files in.

Examples

univariate_cox_model(piu_filename = "/Users/ginny/Google Drive/R_GPD/GPD_package_0401/example/piu_mapping_count.tsv",
                     lu_filename = "/Users/ginny/Google Drive/R_GPD/GPD_package_0401/example/lu_summarising_count.tsv",
                     ncu_filename = "/Users/ginny/Google Drive/R_GPD/GPD_package_0401/example/ncu_summarising_count.tsv",
                     clinical_df = sel_example_cdr,
                     gender_as_covariate = T,
                     race_group_min = 6,
                     min_surv_days = 90,
                     min_surv_people = 5,
                     patient_sum_min = 3,
                     mutation_type = "somatic",
                     output_dir = "/Users/ginny/Google Drive/R_GPD/GPD_package_0401/example/")
                      

ginnyintifa/GPD documentation built on Oct. 23, 2019, 1:52 a.m.