variateExpSingle {YAPSA} | R Documentation |
Application of the likelihood ratio test to mutational signatures, primarily for one single sample.
variateExpSingle( in_catalogue_vector, in_sig_df, in_exposure_vector, in_ind, in_factor = 1, in_pdf = NULL, verbose = FALSE )
in_catalogue_vector |
Mutational catalog of the input sample. |
in_sig_df |
Data frame encoding the signatures used for the analysis. |
in_exposure_vector |
Exposure vector computed for the input sample. |
in_ind |
Index specifying which signature among |
in_factor |
Deviation factor of the altered alternative model. |
in_pdf |
Probability distibution function, parameter passed on to logLikelihood and later to computeLogLik |
verbose |
Verbose if |
Returns a list
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] variateExpSingle( in_ind = 1, in_factor = 1.5, in_catalogue_vector = lymphoma_catalogue_df[, 1], in_sig_df = lymphoma_sig_df, in_exposure_vector = lymphoma_exposures_df[, 1])