decision_deseq2 {exomePeak2}R Documentation

Calculate the decision table for a DESeq2 result.

Description

Decision_dsresult is an internal function used to summary the cut-off and the number of positive results used for DESeq2 result..

Usage

decision_deseq2(
  Inf_RES,
  log2FC_cut = 0,
  P_cut = 0.05,
  Padj_cut = NULL,
  Min_mod = 1000,
  Exp_dir = c("hyper", "hypo", "both")
)

Arguments

Inf_RES

A exomePeak2Results or similar object that contains the result statistics for either methylation or differential methylation.

log2FC_cut

The log2 fold change cutoff of the inference result, default setting is 0.

P_cut

A numeric value between 0 to 1, indicating the p value cut off of the Wald test defined by DESeq2 (or defined by QNB), it will be neglected if Padj_cut is not NULL.

Padj_cut

A numeric value between 0 to 1, indicating the fdr cut off of the Wald test defined by DESeq2 (or defined by QNB).

Min_mod

Minimum number of features returned, when this is smaller than the cut-off results, additional features are called by the order of p values.

Exp_dir

This parameter is filled when making decisions on differential methylation, it could be "hyper", "hypo", and "both".

Value

A data.frame object indicating the column and cut-off value used for desicion, also it includes the number of positive sites in both directions based on the decision.

[Package exomePeak2 version 1.6.1 Index]