produce.cutoff.message {RVA}

Create a message about fold change and pvalues used to produce the plot.

Description

This function processes summary statistics table generated by differential expression analysis like limma or DESeq2 and produces a message about pvalues and fold change used.

Usage

produce.cutoff.message(
  data,
  FCmin,
  FCmax,
  FCstep,
  FDRflag,
  p.min,
  p.max,
  p.step
)

Arguments

data

Summary statistics table from limma or DEseq2, where each row is a gene.

FCmin

The minimum starting fold change cutoff to be checked, so the minimum fold change cutoff to be evaluated will be FCmin + FCstep, FCmin default = 1.

FCmax

The maximum fold change cutoff to be checked, default = 2.

FCstep

The step from the minimum to maximum fold change cutoff, one step increase at a time, default = 0.01.

FDRflag

The column name of the False Discovery Rate (FDR) in the summary statistics table.

p.min

The minimum starting FDR cutoff to be checked, so the minimum fold change cutoff to be evaluated will be p.min + p.step, p.min default = 0.

p.max

The maximum FDR cutoff to be checked, default = 0.2.

p.step

The step from the minimum to maximum fold change cutoff, one step increase at a time, default = 0.005.