Decision_infresult: Calculate the decision table for a DESeq2 result.

In ZhenWei10/meripQC: Quality control and inference for m6A-seq datasets.

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_infresult(Inf_RES, log2FC_cut = 0, P_cut = 0.5, Padj_cut = NULL,
  Min_mod = 10000, DM = FALSE, Exp_dir = NULL, HDER)

Arguments

Inf_RES	A DESeqResults 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.
DM	Whether the result is differential methylation analysis, default is FALSE.
Exp_dir	This parameter is filled when DM = TRUE, can be either "hyper" or "hypo".
HDER	Determine the ID column of the generated table.

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.

ZhenWei10/meripQC documentation built on May 13, 2019, 11:51 p.m.