public class ModelEvaluator
extends java.lang.Object
scope/data/cre/<organism>/
(where
<organism>
is replaced with the name of the organism) and there should be a parameter file called <organism>.param
in ./data/params/
. Each
CRE file should fit the following format:
@ "whitespace-separated list of genes in regulon" # "consensus sequence" $ "tab-delimited position counts for A" $ "tab-delimited position counts for T" $ "tab-delimited position counts for G" $ "tab-delimited position counts for C" > "site" > "site" > "site" ...Lines that don't start with '@', '#', '$', or '>' are ignored.
Results are output to the command line and to an html file.
Modifier and Type | Field and Description |
---|---|
private static int |
FN_AVE |
private static int |
FP_AVE |
private static double[] |
FULL_STRINGENCIES |
private static double[] |
LIST_STRINGENCIES |
private static boolean |
LOG_ODDS |
private static int |
MAX_K |
static int |
MAX_KMM_EXPANSION_SIZE |
private static double[] |
ODDS_STRINGENCIES |
private static int |
PHI_AVE |
private static boolean |
RUN_LISTS |
private static double[] |
STRINGENCIES |
private static boolean |
useWholeGenome |
Constructor and Description |
---|
ModelEvaluator() |
Modifier and Type | Method and Description |
---|---|
private static MotifList |
filterOnStringency(MotifList ml,
double d,
boolean atLeast) |
private static double[] |
initiateMFvars(MotifFinder mf,
boolean discardOverlaps) |
static void |
main(java.lang.String[] args) |
private static final int FN_AVE
private static final int FP_AVE
private static final double[] FULL_STRINGENCIES
private static final double[] LIST_STRINGENCIES
private static final boolean LOG_ODDS
private static final int MAX_K
public static final int MAX_KMM_EXPANSION_SIZE
private static final double[] ODDS_STRINGENCIES
private static final int PHI_AVE
private static final boolean RUN_LISTS
private static final double[] STRINGENCIES
private static boolean useWholeGenome
private static MotifList filterOnStringency(MotifList ml, double d, boolean atLeast)
private static double[] initiateMFvars(MotifFinder mf, boolean discardOverlaps)
public static void main(java.lang.String[] args) throws java.io.IOException, UnknownGeneException
java.io.IOException
UnknownGeneException