confIntExp {YAPSA} | R Documentation |
Compute confidence intervals using the (log-)likelihood ratio test, primarily for one input sample.
confIntExp( in_ind = 1, in_sigLevel = 0.05, in_delta = 1, in_exposure_vector = NULL, in_verbose = FALSE, ... )
in_ind |
Index of the input signature to be variated. |
in_sigLevel |
Significance leve (one-sided) |
in_delta |
Inflation parameter for the alternative model. |
in_exposure_vector |
Exposure vector computed for the input sample. |
in_verbose |
Whether to run verbose (TRUE) or not (FALSE) |
... |
Input parameters passed on to variateExpSingle. |
A list with entries
upper
: Upper bound of the
confidence interval
lower
: Lower bound of the confidence
interval
library(BSgenome.Hsapiens.UCSC.hg19) data(lymphoma_test) data(lymphoma_cohort_LCD_results) data(sigs) word_length <- 3 temp_list <- create_mutation_catalogue_from_df( lymphoma_test_df,this_seqnames.field = "CHROM", this_start.field = "POS",this_end.field = "POS", this_PID.field = "PID",this_subgroup.field = "SUBGROUP", this_refGenome = BSgenome.Hsapiens.UCSC.hg19, this_wordLength = word_length) lymphoma_catalogue_df <- temp_list$matrix lymphoma_PIDs <- colnames(lymphoma_catalogue_df) data("lymphoma_cohort_LCD_results") lymphoma_exposures_df <- lymphoma_Nature2013_COSMIC_cutoff_exposures_df[, lymphoma_PIDs] lymphoma_sigs <- rownames(lymphoma_exposures_df) lymphoma_sig_df <- AlexCosmicValid_sig_df[, lymphoma_sigs] confIntExp(in_ind = 1, in_sigLevel = 0.05, in_delta = 0.4, in_exposure_vector = lymphoma_exposures_df[, 1], in_catalogue_vector = lymphoma_catalogue_df[, 1], in_sig_df = lymphoma_sig_df)