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 0.99.98 Index]