ct.applyAlpha: Apply RRA 'alpha' cutoff to RRAalpha input
In gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

Description Usage Arguments Value Author(s)

The 'alpha' part of RRAalpha is used to consider only the top guide-level scores for gene-level statistics. Practically, all guides failing the cutoff get a pvalue of 1. There are three ways of determining which guides fail. See 'scoring' below.

ct.applyAlpha(
  stats,
  RRAalphaCutoff = 0.1,
  scoring = c("combined", "pvalue", "fc")
)

`stats`	three-column numeric matrix with pvalues for down and up one-sided test with guide-level fold changes (coefficients from the relevant contrast).
`RRAalphaCutoff`	A cutoff to use when defining gRNAs with significantly altered abundance during the RRAa aggregation step, which may be specified as a single numeric value on the unit interval or as a logical vector. When supplied as a logical vector (of length equal to `nrows(fit)`), this parameter directly indicates the gRNAs to include during RRAa aggregation. Otherwise, if `scoring` is set to `pvalue` or `combined`, this parameter is interpreted as the maximum nominal p-value required to consider a gRNA's abundance meaningfully altered during the aggregation step. If `scoring` is `fc`, this parameter is interpreted as the proportion of the list to be considered meaningfully altered in the experiment (e.g., if `RRAalphaCutoff` is set to 0.05, only consider the rankings of the 5 (or downregulated) gRNAs for the purposes of RRAa calculations).
`scoring`	The gRNA ranking method to use in RRAa aggregation. May take one of three values: `pvalue`, `fc`, or '`combined`'. `pvalue` indicates that the gRNA ranking statistic should be created from the (one-sided) p-values in the fit object. `fc` indicates that the ranks of the gRNA coefficients should be used instead, and `combined` indicates that that the coefficents should be used as the ranking statistic but gRNAs are discarded in the aggregation step based on the corresponding nominal p-value in the fit object.