This analysis investigates whether transversions are expected to have a bigger impact on TF binding affinity than transisions. The analysis relies on the JASPAR nonredundant motif set to predift TF binding affinity, and a linear regression analysis to investigate the effects of potential mutations while correcting for each motif and the position of the mutation within each motif.

Performing the analysis is split across two scrips. The first script downloads the nonredundant jaspar database and evaluate the predicted effect on TF affinity of every possible mutation at every possible position in every motif. This analysis is performed by the Effects_on_TFBS_motif_scores.py script.

The second step is the linear regression analyses to ask whether transversions are associated with a bigger effect on TF binding affinity than transitions. That analysis is done in the jaspar_regression_analysis.R script. The output is a log file of overall summary statistics for the data, regression statistics, plots of the regression results, and an R image that canbe loaded for further invstigation. The R code requires that the reshape2 and car packages are installed.

Both steps of the analysis are combined in a simple shell script, jaspar_ts_tv_analysis.sh