Poly(A)-tail gel scanned data to tail distribution statistics
This repository holds code for automated processing of poly(A)-tail gel scanned data to tail distribution statistics for use with poly(A)-tail distributional modelling and fitting
This code converts previously scanned data (in XLS format) into RData files. For format of input XLS file see R script header.
Algorithm is as follows:
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Read whole XLS file containing all lanes
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Then per lane:
- Extract non-empty rows of spreadsheet
- Fit smoothing spline through intensity
- Evaluate spline at lengths 1-600
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Sort lanes in time order
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Build mRNA list variable with following components:
- mRNA: intensity data (intensities>0, otherwise NA)
- times: sorted times from spreadsheet
- time_mask: list of flags per time
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Output RData file with same stem filename as input XLS file
These output files are used by the modelling and parameter fitting codes for obtaining parameters for the poly(A) model.
A test file (test.xls) in the correct format is supplied for code test purposes.
Notes:
- code runs in base R, but uses gdata package to extract Excel data. gdata itself requires a working Perl installation. For Windows, Strawberry Perl works perfectly; for Unix/Linux versions there is a native Perl that should be found if installed correctly when gdata is added to R.