Usage
Basic Usage
Detailed Usage
package "SeekEvaluator"
version "1.0"
purpose "Evaluate results generated from SeekMiner"
section "Mode"
option "single" O "Evaluate one query's rank list result"
flag off
option "aggregate" M "Evaluate multiple queries and aggregates results"
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option "multi_weight" T "Evaluate multiple queries' dataset weight files"
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section "Metric"
option "fixed_pr" z "Precision at depth X"
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option "rbp" r "Rank biased precision (requires parameter p to be set)"
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option "avgp" a "Average precision for the top X positives, where X = integer, or % of total positives"
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option "pr" t "Precision at X-th positive, where X = integer, or % of total positives"
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option "pr_all" c "Precision at all positive depths (useful for drawing precision-recall curve)"
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option "auc" u "AUC"
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option "x_int" x "Parameter X = integer, for --avgp, --pr"
int default="-1"
option "x_per" e "Parameter X = percentage, for --avgp, --pr"
float default="0"
option "rbp_p" p "Parameter p, for --rbp"
float default="0.95"
option "dislay_only" F "Display the genes sorted by score (top 500 is shown, for single mode only)"
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option "display_weight" W "Display dataset weights (top 100)"
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section "Aggregator (for multi-query evaluation)"
option "agg_avg" A "Show the average, standard deviation of the metric for all queries"
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option "agg_quartile" B "Show the min, max, as well as the 1st, 2nd, 3rd quartile of the metric for all queries"
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option "agg_ranksum" C "Sum up the ranks of genes in all query rankings to produce a master list sorted by summed rank, and perform metric on this list"
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option "agg_scoresum" D "Sum up the scores of genes in all query rankings to produce a master list sorted by summed score, and perform metric on this list"
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option "display_all" E "Display the metric for all queries"
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section "Input required by all"
option "input" i "Gene mapping file"
string typestr="filename" yes
section "Input required by dataset weight display (single .dweight file)"
option "dataset_map" I "Dataset mapping file, only required for displaying dataset weights"
string typestr="filename"
option "weight" w "Dataset weight file, (*.dweight)"
string typestr="filename"
section "Input required by multi-query dataset weight display"
option "dweight_list" Z "List of dweight files"
string typestr="filename"
section "Options for all"
option "fold_over_random" f "Fold-over-random"
flag off
option "p_value" P "Simulated p-value"
flag off
option "random_dir" R "Random directory"
string typestr="directory"
option "random_num" N "Number of random trials"
int default="100"
section "Input required by single-query"
option "goldstd" s "Gold standard gene set file (one line, space delimited)"
string typestr="filename"
option "gscore" g "Gene score file (.gscore)"
string typestr="filename"
option "query" q "Query gene set file (to be excluded from evaluation) (.query)"
string typestr="filename"
option "exclude" y "Exclude genes (.exclude)"
string typestr="filename"
option "nan" n "Define NaN score"
float default="-320"
section "Input required by multi-query"
option "goldstd_list" S "List of gold standard gene set files"
string typestr="filename"
option "gscore_list" G "List of gene score files"
string typestr="filename"
option "query_list" Q "List of query gene set files"
string typestr="filename"
option "exclude_list" X "Exclude gene list"
string typestr="filename"
option "include_list" Y "List of annotated genes"
string typestr="filename"
section "Output"
option "dir_out" d "Output directory"
string typestr="directory" yes
| Flag | Default | Type | Description |
| -i | stdin | Text file | Tab-delimited text file containing two columns, numerical gene IDs (one-based) and unique gene names (matching those in the input DAT/DAB files). |
| -d | . | Directory | Input directory containing DB files |
| -D | . | Directory | Output directory in which database files will be stored. |
| -x | . | Text file | Input file containing list of CDatabaselets to combine |
