All functions
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annotate_cc_list()
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Call AnnotationGenerator on a list of data |
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AnnotationGenerator()
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generate case control annotations for hit data based on library annotation file. |
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AVARDA_RCPGenerator()
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calculate RCP for AVARDA data |
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compute_rcp_list()
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Calculate relative control percentile statistic for a list of data. |
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compute_stats_list()
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calculate statistics for list of data |
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config_case_control()
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setup configurations for this case control study |
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define_plan_case_control()
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Setup drake plan for case control report targetse. |
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filter_hits()
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filter hits data to prepare for RCPGenerator |
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filter_hits_list()
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filter hits for data list. |
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gather_sample_list()
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Return a list of subsetinput data based on specified data types, file paths,
and sample names. |
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generate_clustergram()
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generates clustergram of hits |
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phipcc
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phipcc: case control reports for PhIP-Seq. |
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plot1_hitfreq()
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Plot hit frequency vs median hit score of cases |
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plot2_hitscore()
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second plot |
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plot3_pval()
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third plot |
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prepare_AVARDA_candidate_table()
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prepare_AVARDA_candidate_table |
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prepare_AVARDA_candidate_table_html()
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prepare_AVARDA_candidate_table_html |
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prepare_AVARDA_clustergram_data()
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prepare_AVARDA_clustergram_data |
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prepare_candidate_table()
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candidate antigen generator script |
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prepare_candidate_table_html()
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Add kable html stying to candidate table. |
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prepare_clustergram_data()
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Process hit data for hierarchical clustering. |
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prepare_epitope_clustergram_data()
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Collapse hit clustergram based on cross-reactive peptide groups defined by epitopefindr. |
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RCPGenerator()
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RCPGenerator calculates RCP, Relative Control Percentile, a case-control
statistic describing the percentile from 0.0 to 1.0 of one score against
that of a control population. For example, if a control population consisted
of three scores, 4.1, 5.0, 6.8, and 10.1, then a score of 5.0 would be
assigned an RCP of 0.25, because 5.0 is higher than 25
population. In this implementation, ties count as losses. |
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read_AVARDA()
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read_AVARDA |
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render_from_template()
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Pass parameters to R markdown case control template and knit html output file. |
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StatsGenerator()
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performs a first round of
calculations on the data such as hit frequency and Fisher's test. These
calculations will be used in subsequent graphing. |
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StatsGenerator_AVARDA()
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generate statistics from AVARDA output |
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subset_AVARDA()
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subsetAVARDA |
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subset_data()
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subset data to only contain rows that match a template. |