R Script prep for GOplot from Trinity

This post contains an adapted R script based on prep_n_run_GOplot.pl from Trinity, the denovo transcriptome assembler, for the times R cannot read in the produced EC.* files. prep_n_run_GOplot.pl is used to produce GOplot visualizing differential expression, sorted by GO terms (see http://wencke.github.io/). It uses the DE_analysis.DE_subset and DE.subset.GOseq.enriched files to produce two other files, EC.david. and EC.genelist used in GOplot. In most cases, this script words properly. However, sometimes when the text annotation contains special characters such as , EC.