This function performs cancer detection based on indel information from a BAM file using a predefined list of mutations. It processes the mutations data and uses the provided model to make cancer calls.
dreams_cc_indels(
mutations_df,
bam_file_path,
reference_path,
model,
model_indels,
alpha = 0.05,
calculate_confidence_intervals = FALSE,
use_turboem = TRUE
)
A dataframe containing the list of mutations to be analyzed.
Path to the BAM file containing sequencing data.
Path to the reference genome file, typically in FASTA format.
The model to be used for cancer detection.
The model to be used for calling mutations for indels.
Significance level for statistical testing, default is 0.05.
Logical flag indicating whether to calculate confidence intervals, default is FALSE.
Logical flag indicating whether to use the turboEM algorithm, default is TRUE.
A list()
with:
cancer_info A data.frame()
with results for cancer calling across all mutations:
The estiamted tumor fraction (allele fraction).
The confidence interval of tf_est
.
The estiamted fraction/number of candidate mutations present in the sample.
The confidence interval of r_est
.
Number of candidate mutations tested.
Total count and coverage across all mutations (only reference and alternative allele(s).
Number of candidate mutations tested.
If the EM algorithm converged.
Number of steps and function evaluations by the EM algorithm.
The value of the log-likelihood function under the null (tf=0) and alternative (tf>0) hypothesis.
The chisq test statistic, degrees of freedom and p-value of the statistical test.
Whether cancer was detected at the supplied alpha level.
mutation_info A data.frame()
with information about the individual mutations:
The genomic position of the mutation.
The reference and alternative allele.
The estimated probability the mutation is present in the sample.
The expected count of the alternative allele under the error (null) model.
The count of the alternative allele.
The coverage used by the model (only referenceredas with and alternative allele).
The observed frequency of the alternative allele.