The script development team at Golden Helix has been hard at work these past few months and this means several new and exciting tools for our SVS customers!  The scripts featured in this blog post vary in function, from expanding the analytical options currently offered in SVS to transforming and editing spreadsheets.  As always, we invite you to visit our scripts repository to download these scripts and documentation and also to browse our other offerings.

Expanded Analysis Features

There are four new analysis scripts available: Chisquared Test with Continuity Correction, Correct P-values for Multiple Tests, Calculate Pseudo Lambda, and Absolute Risk Reduction. You will find a small description for each script below.  For more information about the nuts and bolts behind the scripts and for usage instructions, please view the PDF documentation available on each script’s download page.

• Chisquared Test with Continuity Correction: Performs a chi-square test with 3 optional genetic models and adjusts p-values with the Yates continuity correction.  The output contains results both before and after applying the continuity correction as well as cell counts given the selected genetic model.
• Correct P-values for Multiple Tests: This column script calculates Bonferroni and FDR adjusted p-values from a p-value column.  This feature allows the user to apply the multiple-testing penalty without having to rerun the analysis.
• Calculate Pseudo Lambda: This feature calculates a pseudo Lambda value for p-value columns that were not derived from a chi-squared statistic.  This script estimates the value using -log10 p-values.
• Absolute Risk Reduction: A new analysis feature that calculates the absolute risk reduction of a treatment and disease set.

Spreadsheet Manipulation

In many of our customer collaboration projects, organizing and manipulating a dataset generally composes the bulk of the workload.  With this in mind, we are always thinking about new ideas for automated tools to make this process as painless as possible.  The tools described below may help you streamline this sort of work in your own research.

• Inactivate Duplicate Column Headers: This script inactivates additional occurrences of column headers, leaving only the first occurrence active.
• Move Columns to Location: This script moves all columns of a specified type to a specified location (beginning or end). This tool can be used to group like column types.
• Quantile Transformation: This script transforms a numeric column into N user-specified quantiles.
• Convert Dosages to Genotypes: This tool converts dosage data (in a variety of formats) into genotypes based on user-specified thresholds.

Is there a tool missing from your toolbox?  Our Bioinformatic Support Team wants to hear your ideas!  Send us an email with your feature request or call us and talk to a real person (888-589-4629)!