cal.pathway.scores {RVA}

calculate pathway scores

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.