logLikelihood {YAPSA} | R Documentation |
Compute a likelihood ratio test based on the loglikelihoods of the residuals of two different models of the same data.
logLikelihood( in_1, in_2, df_1 = NULL, df_2 = NULL, in_pdf = NULL, verbose = FALSE )
in_1 |
Residuals of model 1 of the input data. |
in_2 |
Residuals of model 2 of the input data. |
df_1 |
Degrees of freedom of the input model 1. If either |
df_2 |
Degrees of freedom of the input model 2. If either |
in_pdf |
Probability distribution function, passed on to computeLogLik, if NULL a normal distribution is used. |
verbose |
Verbose if |
A list with entries
statistic
: The test
statistic
delta_df
: The difference in degrees of freedom between
input model 1 and 2
p.value
: p value of the statistical test.
library(BSgenome.Hsapiens.UCSC.hg19) data(lymphoma_test) data(sigs) data(cutoffs) 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) current_sig_df <- AlexCosmicValid_sig_df current_sigInd_df <- AlexCosmicValid_sigInd_df current_cutoff_vector <- cutoffCosmicValid_rel_df[6, ] iniLCDList <- LCD_complex_cutoff( in_mutation_catalogue_df = lymphoma_catalogue_df[, 1, drop = FALSE], in_signatures_df = current_sig_df, in_cutoff_vector = current_cutoff_vector, in_method = "relative", in_rescale = TRUE, in_sig_ind_df = current_sigInd_df) current_sig_df <- AlexCosmicValid_sig_df[, -9] current_sigInd_df <- AlexCosmicValid_sigInd_df[-9,] current_cutoff_vector <- cutoffCosmicValid_rel_df[6, -9] redLCDList <- LCD_complex_cutoff( in_mutation_catalogue_df = lymphoma_catalogue_df[, 1, drop = FALSE], in_signatures_df = current_sig_df, in_cutoff_vector = current_cutoff_vector, in_method = "relative", in_rescale = TRUE, in_sig_ind_df = current_sigInd_df) logLikelihood(iniLCDList, redLCDList)