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Whistle Requirements

• BEL Framework 3.0.0 or higher
• A KAM (Knowledge network)
• A data input file in IdAMP format

Command-line arguments

Required arguments

These arguments must be provided:

Short option	Long option	Description
-f	--input-file	Data set input file in IdAMP format.
-k	--kam	KAM name. Must be present in the local KAM catalog.
-r	--run-name	This input will be used as a prefix for output files.
-u	--namespace-url	Resource location URL of the data set's BEL namespace.

One of the following sets of argument(s) must be provided:

-s, --use-analyst-selection

Identify differentially expressed genes based on provided flag in [As] column of data.

-m, -p, AND -a

As alternate to analyst selection, fold change, p-value, and abundance thresholds must be provided to use for determining differentially expressed genes.

Short option	Long option	Description
-s	--use-analyst-selection	Use [As] column to identify differentially expressed genes.
-a	--abundance-cutoff	Abundance cutoff to apply to measurements.
-m	--fold-change-cutoff	Fold change cutoff to apply to measurements.
-p	--p-value-cutoff	p-value cutoff to apply to measurements.

Optional arguments

-t, --taxid

Use to select a species by taxid: human = 9606, mouse = 10090, rat = 10116. If a taxid is provided, orthologous nodes in the KAM will be collapsed to the selected species.

-detail

Output two additional files, a mapping file indicating how each measurement in the data file maps to the KAM and a details file which provides detailed scoring information for each mechanism.

-n, --population-size

Use to override the default population size (based on the values in the Id column and RNA abundance nodes in the selected KAM). The population size is used to calculate richness.

Sample runs

Windows, using analyst selection, orthologizing to human, and optional detail files:

whistle.cmd -r test_run -f GSE2638.csv -s -k "Large Corpus" -u   http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u133ab.belns -t 9606 -detail

Linux or OS X, using fold change, p-value, and abundance thresholds:

./whistle.sh -r test_run -f GSE2638.csv -k "Large Corpus" -u http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u133ab.belns -a 5 -m 1.3 -p 0.05

Whistle Outputs

population size

Calculated based on specified KAM and measurements provided in input data file.

number of state changes

Number of differentially expressed genes (based on analyst flag or user-specified abundance, p-value, and fold-change cutoffs)

number of Scores

Number of small networks produced from the selected KAM and evaluated by Whistle

results file

.csv file with scores for each small network evaluated

mapping file

(optional, provided if -detail argument used) .csv file with information about how each data measurement maps to the KAM

mechanism details file

(optional, provided if -detail argument used) .csv file with detailed scoring information for each mechanism