cal.pathway.scores: calculate pathway scores

In RVA: RNAseq Visualization Automation

Description

Calculate pathway scores

Usage

cal.pathway.scores(
  data,
  pathway.db,
  gene.id.type,
  FCflag,
  FDRflag,
  FC.cutoff,
  FDR.cutoff,
  OUT.Directional = NULL,
  IS.list = FALSE,
  customized.pathways,
  ...
)

Arguments

data	A summary statistics table (data.frame) or data.list generated by DE analysis software like limma or DEseq2
pathway.db	pathway database used
gene.id.type	gene.id.type
FCflag	The column name (character) of fold change information, assuming the FC is log2 transformed. Default = "logFC".
FDRflag	The column name (character) of adjusted p value or FDR. Default = "adj.P.Val".
FC.cutoff	The fold change cutoff (numeric) selected to subset summary statistics table. Default = 1.5.
FDR.cutoff	The FDR cutoff selected (numeric) to subset summary statistics table. Default = 0.05.
OUT.Directional	logical, whether output directional or non-directional pathway analysis result, default: NULL.
IS.list	logical, whether the input is a list, default: NULL
customized.pathways	the customized pathways in the format of two column dataframe to be used in analysis
...	pass over parameters

Value

Returns a dataframe.

References

Xingpeng Li & Siddhartha Pachhai RVA - RNAseq Visualization Automation tool.

RVA documentation built on Nov. 2, 2021, 1:06 a.m.