Code for resolving swaps and adding the phenotype info

[lcolladotor]

Write a Rmd file (under it's own directory) similar to those from http://leekgroup.github.io/recount-analyses/ https://github.com/leekgroup/recount-analyses (using BiocStyle and knitcitations; use here::here() for paths) where you read in the output data from SPEAQeasy (the inferred genotype info) + the DNA genotype info (as downloaded from #3 ) to then:

• find if there are swaps
• classify the swaps into simple and complex
• drop complex and resolve simple (manually)

The main output should be a RangedSummarizedExperiment object with the correct phenotype information for the samples (include all the colData() output from SPEAQeasy + add the phenotype info we have on the brains after resolving the simple swaps).