Man pages for lindberg-m/contextendR
Analyse genomic data with regard to sequence contexts
| binary_enc | Encode a character vector into a binary matrix |
| count_kmers | Count kmers |
| count_trinucs | Calculate trinucleotide frequency |
| encode_seqs | Encode sequences into binyary format |
| extend_positions | Add nucleotide positions and extract sequence contexts |
| get_logenv | Get logging environment |
| get_n_warnings | Get n warnings |
| handle_condition | Handle conditions and logging |
| handle_try_catch | Hanle possible errors and warnings |
| inverse_logit | Inverse logit |
| kmer_freq | Kmer frequency |
| kmer_logistic_regression | Fit regularized multinomial regression model |
| kmer_random_forest | Score kmer-importance through a random forest |
| melanoma_mutations_promoters | Genomic positions of single nucleotide variants in melanoma... |
| plot_kmer_forest | Plot Feature Selection Results |
| plot_kmer_logistic_regression | Plot results from a fitted 'kmer_logistic_regression' |
| plot_kmer_positions | Plot positional effects of kmers |
| plot_trinuc_logistic_regression | Plot results from a fitted 'kmer_logistic_regression' |
| promoters | Promoter regions in hg19 saved as a GRanges object |
| reset_n_warnings | Reset n warnings |
| sample_positions | Sample random posiotions from the genomic regions supplied. |
| set_logfile | Set logfile |
| set_logging_tee | Set loggin Tee |
| set_loglevel | Set loglevel |
| unset_logfile | Set logfile |
| unset_logging_tee | Unset logging Tee |
