diff ttest/stats.xml @ 0:12bb38e187b9

Uploaded, initial check-in

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ttest/stats.xml	Mon Jul 28 20:12:17 2014 -0400
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+<tool id="ucscCancerBrowserStats" description="Statistical Tests of Difference" name="UCSC Cancer Browser Stats" version="0.0.1">
+  <description>Apply statistical tests of difference to the rows in a genomic matrix, where the columns are categorized by a second (clinical) matrix</description>
+  <command interpreter="python">
+    stats.py  $genomicMatrix $clinicalFeatures $outFile -a="${category1}" -b="${category2}"
+  </command>
+  <inputs>
+    <param format="tabular" name="genomicMatrix" type="data" label="Genomic Matrix"/>
+    <param format="tabular" name="clinicalFeatures" type="data" label="Clinical Matrix"/>
+    <param type="text" name="category1" label="Category 1" optional="false"/>
+    <param type="text" name="category2" label="Category 2" optional="false"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="outFile" />
+  </outputs>
+  <requirements>
+    <requirement type="python-module">numpy</requirement>
+  </requirements>
+  <tests>
+    <param name="genomicMatrix" value="sample.genomic.matrix.txt"/>
+    <param name="clinicalMatrix" value="sample.clinical.matrix.txt"/>
+    <param name="category1" value="A"/>
+    <param name="category2" value="B"/>
+    <output name="outFile" value="sample.stats.output.txt"/>
+  </tests>
+  <help>
+
+This tool performs statistical tests found in the UCSC Cancer Genomics
+Browser.  The input data is a genomic matrix (containing genomic data,
+with rows representing genes or probes and columns representing
+samples or patients), a clinical matrix of two (or more) columns
+assigning categorical values to the samples, and two categorical
+values of interest.  The tool identifies the samples corresponding to
+each categorical value, then identifies the columns in the genomic
+matrix corresponding to those sets of samples, which identifies two
+groups of columns.  For each row in the genomic matrix, it extracts
+the value for those two sets of columns, performs a t-test on the two
+sets of values, and returns the result for the row.  Any values for
+any columns NOT pertaining to one of the categorical values of
+interest are ignored.
+
+The user runs this tool with th following steps:
+
+
+1. Specify a genomic matrix.  The expected format is with rows representing 
+genes and columns representing samples, and the first line contains sample 
+names.
+
+2. Specify a clinical matrix.  Here, rows indicate samples, columns
+indicate clinical features, and the header row contains feature names.
+The first column MUST indicate the sample names, and MUST correspond
+to the column names of the genomic matrix.  The clinical feature of
+interest MUST be in the second column.  Any other columns will be
+ignored.
+
+
+3. Indicate two clinical values that you want to use for defining the
+two groups.  For example, the two groups could be "Red group" and
+"Green group", 0 and 1, or whatever.
+
+The output indicates, for each row, the t-statistic reporting on the
+difference between the two groups of columns (as specified by the two
+clinical values), the p-value corresponding to that t-statistic, the
+median value for each group, and the difference between the medians.  If it 
+cannot calculate these values, it returns a vector of NAs.
+
+For example, given the following genomic matrix for (1)::
+
+    Gene  1    2    3    4    5    6    7    8    9    10
+    G1    2.0  2.2  3.2  1.1  5.1  8.1  3.2  1.1  8.1  0.2
+    G2    0.1  8.2  9.1  4.2  6.1  4.9  3.9  2.3  1.1  0.2
+
+and given the following clinical matrix for (2)::
+
+    sample_id Value
+    1         A
+    2         A
+    3         B
+    4         C
+    5         B
+    6         B
+    7         A
+    8         A
+    9         B
+    10        A
+    
+and given A for Category 1 and B for Category 2
+
+the tool will assemble the following two groups of values::
+
+    G1 A:(2.0, 2.2, 3.2, 1.1, 0.2) B:(3.2, 5.1, 8.1, 8.1)
+    G2 A:(0.1, 8.2, 3.9, 2.3, 0.2) B:(9.1, 6.1, 4.9, 1.1) 
+
+Note that the values for sample_id 4 do not appear, because it has a Value
+of C in the second column, which is neither A nor B.
+
+And it will return the output::
+
+    Gene Statistic  pValue    Median1   Median2   Delta
+    G1   -4.168999  0.004194  2.000000  6.600000  -4.600000
+    G2   -1.198486  0.269724  2.300000  5.500000  -3.200000
+
+
+  </help>
+</tool>