surf: Statistical Utility for RBP (RNA binding protein) Functions

Builds the "rankings" for each sample: expression-based ranking for all the genes/transcripts in each sample. The genes/transcripts with same expression value are shuffled. Therefore, genes/transcripts with expression '0' are randomly sorted at the end of the ranking. These "rankings" can be seen as a new representation of the original dataset. Once they are calculated, they can be saved for future analyses.

getRankings(
  exprMat,
  plotStats = FALSE,
  cores = max(1, detectCores() - 2),
  verbose = FALSE
)

`exprMat`	Expression matrix (genes/transcripts as rows, samples as columns). The expression matrix can also be provided as one of the Bioconductor classes: RangedSummarizedExperiment and derived classes: The matrix will be obtained through `assay(exprMat)`, -which will extract the first assay (usually the counts)- or the assay name given in `assayName` dgCMatrix-class: Sparse matrix `ExpressionSet`: The matrix will be obtained through `exprs(exprMat)`
`plotStats`	Should the function plot the expression boxplots/histograms? (TRUE / FALSE). These plots can also be produced with the function `plotGeneCount`.
`cores`	`integer`, number of computing workers.
`verbose`	`logical`, whether (`TRUE`) to echo progress.