Add go annotations to szannotation or its cross-reference
for every entry in szGoPortion
delimited by tabs, semiclons, commas, pipes, or double quotes.
Adds szcategory or its alternative ID to gocategories, provide it is not in removedterms
also if this category has not been seen before add the ID and its name if available to htGO.
If repeat data comes from distinct time series (true) that is a longitudal time series,
otherwise it is false and each column of the same time point between data sets is interchangeable
True if gene change threshold for filtering is based on the max-min difference
False if the gene change threshold for filtering is based on the absolute difference
Builds the initial tree which is just a single chain with mean and standard
deviation for each node being the global mean and standard deviation at
the time point
Uses DREM_NaiveBayes to build a classifier which predicts given the set of transcription
factors predicted to regulate a gene whether it would appear filtered or not
A control method that handles the response for when the execute button on the interface is pressed
including building the data set, running the DREM modeling procedure, and displaying the results
Sets up the stored data so that the training data includes all data except any external held out validation
data, meaning the data which might otherwise used for model selection is just for parameter learning
Class encapsulates information on the comparison of two STEM data sets
focusing on identifying pairs of profiles with significant intersections
between them.
Updates the G parameters in the multi-class case
bnew means the coefficient changed on the previous coordinate or first time
if didn't change then can keep previous errors just update current coefficient
bfirsttime means it is the first pass through the coeffienients
Updates the value of the G matrix for the binary case
bnew means the coefficient changed on the previous coordinate or first time
If didn't change then can keep previous errors just update current coefficient
bfirsttime means it is the first pass through the coefficients
Computes association scores for the transcription factors overall on paths and
on paths out of splits conditional on the set of genes going into the split
Returns true if an entry in sztaxonval is also an entry in szTaxon
or after prepending a 'taxon:'
szTaxon entries are delimited by pipes
sztaxonval entries are delimited by semicolons, commas, and pipes
Computes correlation coefficient between xvalues and yvalues only for those that
have non-zero includex and includey values
Returns 0 if no values are agree on for all data
Computes correlation coefficient between xvalues and yvalues only for those that
have non-zero includex and includey values
Returns 0 if no values are agree on for all data
Encapsulates a table providing information on GO enrichments for the sets of genes on paths
out of splits conditioned on the set of genes going into the split
Filters those rows which do not have a true in keepgene
nkeep is the number of true rows in keepgene
If bstore is true and gene is filtered then we stroe the gene
and proble list for it in htFiltered
Returns a new DataSetCore object with those rows filtered
If bmaxminval is true, then
filter those genes for which the difference between the max and min
value is less than dthresholdvalue
If bmaxminval if false, then
filter those genes for which the absolute expression change is less
than dmaxval
Returns true if the gene ID szID is of type szCategory
any sub entry or the entire string could match where entries
are delimited by semicolons, pipes, or commas
Present/missing data for several data sets
First dimension is gene
Second dimension is repeat
Third dimension is spot
Fourth dimension is expression value (in log ratio form against time zero)
Present/missing data for several data sets
First dimension is gene
Second dimension is repeat
Third dimension is spot
Fourth dimension is present/missing value
Returns the GO results for actual size based enrichment for a set
where the indicies of the set of genes in the set is ids
If bqueryset is true, then only genes also in the query set will be used
If htinames is non-null, then only genes also in htinames will be used
Returns the GO results for expected size based enrichment for a set
where the indicies of the set of genes in the set is ids
If dexpected is <0, returns an actual size based enrichment
If bqueryset is true, then only genes also in the query set will be used
If htinames is non-null, then only genes also in htinames will be used
Used to get the GO results for a cluster of profiles
the id of each profile in the cluster is listed in profileList
an array list in ids has all the indicies in genenames
assigned to the profile
If bqueryset is true, then only genes also in the query set will be used
If htinames is non-null, then only genes also in htinames will be used
Returns the probability of seeing more than x objects of type A, when there are nA objects of type A
nB objects of type B, and nm objects total drawn
This can be used to compute a more accurate p-values than a 1-cumulative probability calculation
Combines the results of the forward and backward algorithm to obtain the probability of
each gene going through each state when using baum-welch training
Generates pvalTF and pvalTFindex based on pval and pvalindex so that the rows correspond to each TF
and each entry in a row pvalTFindex corresponds to an index of a gene the TF regulates and the corresponding
entry in pvalTF corresponds to the interaction value
Used to set probability of each state a gene with a TF-binding signature of binding will be in
Also computes a record of other statistics based on these predictions
Class for manipulating layout
Code from
http://java.sun.com/docs/books/tutorial/uiswing/examples/layout/SpringGridProject/src/layout/SpringUtilities.java
here is the copyright for that code
Copyright (c) 1995 - 2008 Sun Microsystems, Inc.
Class implements a record for a profile, storing its ID,
the number of genes assigned, the number of genes expected,
and the uncorrected p-value of the number of genes assigned versus expected
This class is a modifed version of the Java TableSorter class
http://java.sun.com/docs/books/tutorial/uiswing/examples/components/TableSorterDemoProject/src/components/TableSorter.java
Copyright for this sample code
==============================================================
Copyright (c) 1995 - 2008 Sun Microsystems, Inc.
Iterates over all the entries in htGoCounts seeing if the
current enrichment beats the enrichment in hIDpval for either the actual
size enrichment or expected size enrichment and if so updates it