Man pages for fosterlab/CFTK
The Co-Fractionation Toolkit
| as_annotation_list | Convert a data frame to a list of gene sets |
| binomial | Calculate the co-dependency index |
| calculate_complex_auc | Evaluate the recovery of known protein complexes |
| calculate_features | Calculate and merge features for a list of CF-MS matrices |
| calculate_go_auc | Evaluate the recovery of proteins annotated to the same GO... |
| calculate_precision | Calculate precision at each point in a sequence |
| combine_matrices | Combine multiple CF-MS matrices into a single matrix |
| cor.fk.nz | Fast calculation of Kendall's tau rank correlation... |
| dice | Calculate the Dice distance between all columns in a matrix |
| filter_matrix | Filter low-quality chromatograms from a CF-MS chromatogram... |
| filter_pairs | Filter protein pairs from a chromatogram score matrix |
| gaf_colnames | Column names for a GAF file |
| get_splits | Split a set of reference protein-protein interactions into... |
| go_roots | Roots of the Gene Ontology |
| hamming | Calculate the Hamming distance between all columns in a... |
| impute_missing_features | Impute missing features with the median, plus or minus some... |
| jaccard | Calculate the Jaccard index between all columns in a matrix |
| kendall_zi | Calculate the estimator of Kendall's tau for zero-inflated... |
| label_pairs | Make labels for a list of protein pairs based on a gold... |
| merge_features | Merge features across multiple replicates |
| metrics | Metrics available in the CFTK |
| plot_pr | Plot a precision-recall curve for a list of protein-protein... |
| plot_roc | Plot a ROC curve for a list of protein-protein interactions |
| read_corum | Read complexes from the CORUM database |
| read_gaf | Read a GAF file |
| read_maxquant | Read CF-MS data from MaxQuant |
| replace_missing_values | Replace missing values in a CF-MS chromatogram matrix |
| sanitize_missing_values | Sanitize missing values in a CF-MS chromatogram matrix |
| score_interactions | Score potential interactions in cross-validation |
| score_pairs | Score the similarity of all pairs of chromatograms |
| threshold_precision | Threshold interactions at a given precision cutoff |
| to_adjacency_matrix | Create an adjacency matrix from a pairwise data frame |
| to_pairwise_df | Convert an annotations list to a pairwise data frame |
| transform_matrix | Log-transform or quantile normalize a CF-MS matrix |
| wtd_rank | Implement weighted rank correlation, as described in Jerrold... |
