Tabulate.exe
This program takes data containing pValues from both real and null experiments and produces qValues for the real cases.
Usage:
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 fileThere 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
Options
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
narrowInputFileNamePattern1{+narrowInputFileNamePattern2...}
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