This program takes data containing pValues from both real and null experiments and produces qValues for the real cases.


Tabulate -help
Tabulate {-NoAudit} {-MaxPValue maxPValue} {-KeepTest keeptest} inputFile1 {inputFile2 ...} outputFile
Tabulate {-NoAudit} {-MaxPValue maxPValue} {-KeepTest keeptest} broadInputFilePattern1 {broadInputFilePattern2 ...} outputFile

Simple Example

Tabulate -NoAudit -MaxPValue .05 Input\03052007.pValues.txt TempOutput\03052007.qValues.txt

Input File Format

The input file(s) should be tab-delimited text files. The input can contain any columns but must include the columns "NullIndex"and "PValue".

For example:

AnyColumn1 NullIndex AnyColumn2 AnyColumn3 PValue AnyColumn4
anyValue1 -1 anyValue2 anyValue3 0.015117191 anyValue4
anyValue1 -1 anyValue2 anyValue3 0.00142628 anyValue4
... ... ... ... ... ...
anyValue1 0 anyValue2 anyValue3 0.021228701 anyValue4

Full file

There should be one row per experiment. All the real results should have a null index of "-1". All the null results should have a null index of 0 or greater.

Output File Format

The output file will be a tab-delimited text file. All columns will be same as the input with the addition of a new column called "qValue". All real rows will appear in the output. All null rows will be filtered out. The rows will be sorted by pValue.

For example:

AnyColumn1 NullIndex AnyColumn2 AnyColumn3 PValue AnyColumn4 qValue
anyValue1 -1 anyValue2 anyValue3 8.60E-05 anyValue4 0
anyValue1 -1 anyValue2 anyValue3 0.00018431 anyValue4 0
anyValue1 -1 anyValue2 anyValue3 0.000606515 anyValue4 0
anyValue1 -1 anyValue2 anyValue3 0.00123407 anyValue4 0.25
... ... ... ... ... ... ...

Full file


By default, "Tabulate" will audit the "rowIndex" and "rowCount" values
in the input to remove duplicates and check that all rows are present.
Use "-NoAudit" when this is not desired.

Use "-MaxPValue maxPValue", where maxPValue is a double, to ignore rows with obviously bad rows

-KeepTest keepTest, default, AlwaysKeep

Name Patterns

Each broadInputFileNamePattern1 is of the form

Each broadInputFileNamePattern must cover the same range of nullIndexes (including -1, the real index).

Each narrowInputFileNamePattern within a broadInputFileNamePattern must cover a disjoint
set of nullIndexes.

Tabulate -MaxPValue .05 raw\GagEscape0606*-1-19*.txt raw\GagReversion0606*-1-9*.txt+raw\GagReversion0606*10-19*.txt AllGag.qValue.txt
Notice that broad pattern
  • raw\GagEscape0606*-1-19*.txt
has one narrow pattern and covers nullIndex's -1 to 19

While broad pattern
  • raw\GagReversion0606*-1-9*.txt+raw\GagReversion0606*10-19*.txt
has two narrow patterns:
  • raw\GagReversion0606*-1-9*.txt, which covers nullIndexes -1 to 9
  • raw\GagReversion0606*10-19*.txt which covers nullIndexes 10 to 19

Last edited Apr 20, 2007 at 12:37 AM by CarlK, version 28


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