decision_deseq2: Calculate the decision table for a DESeq2 result.
In exomePeak2: Bias Awared Peak Calling and Quantification for MeRIP-Seq

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

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

`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".

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.

exomePeak2 documentation built on Nov. 8, 2020, 5:27 p.m.