Man pages for brandonsie/phipcc
Generate Case-Control Reports from PhIP-seq Data
| annotate_cc_list | Call AnnotationGenerator on a list of data |
| AnnotationGenerator | generate case control annotations for hit data based on... |
| AVARDA_RCPGenerator | calculate RCP for AVARDA data |
| compute_rcp_list | Calculate relative control percentile statistic for a list of... |
| compute_stats_list | calculate statistics for list of data |
| config_case_control | setup configurations for this case control study |
| define_plan_case_control | Setup drake plan for case control report targetse. |
| filter_hits | filter hits data to prepare for RCPGenerator |
| filter_hits_list | filter hits for data list. |
| gather_sample_list | Return a list of subsetinput data based on specified data... |
| generate_clustergram | generates clustergram of hits |
| phipcc | phipcc: case control reports for PhIP-Seq. |
| plot1_hitfreq | Plot hit frequency vs median hit score of cases |
| plot2_hitscore | second plot |
| plot3_pval | third plot |
| prepare_AVARDA_candidate_table | prepare_AVARDA_candidate_table |
| prepare_AVARDA_candidate_table_html | prepare_AVARDA_candidate_table_html |
| prepare_AVARDA_clustergram_data | prepare_AVARDA_clustergram_data |
| prepare_candidate_table | candidate antigen generator script |
| prepare_candidate_table_html | Add kable html stying to candidate table. |
| prepare_clustergram_data | Process hit data for hierarchical clustering. |
| prepare_epitope_clustergram_data | Collapse hit clustergram based on cross-reactive peptide... |
| RCPGenerator | RCPGenerator calculates RCP, Relative Control Percentile, a... |
| read_AVARDA | read_AVARDA |
| render_from_template | Pass parameters to R markdown case control template and knit... |
| StatsGenerator | performs a first round of calculations on the data such as... |
| StatsGenerator_AVARDA | generate statistics from AVARDA output |
| subset_AVARDA | subsetAVARDA |
| subset_data | subset data to only contain rows that match a template. |
