newspia {PMAPscore}

newspia

Description

Function 'newspia' This function is based on SPIA algorithm to analyse KEGG signal pathway for single sample..

Usage

newspia(
  de = NULL,
  all = NULL,
  organism = "hsa",
  data.dir = NULL,
  pathids = NULL,
  verbose = TRUE,
  beta = NULL
)

Arguments

de

A named vector containing the statue of particular genes in a particular sample.The names of this numeric vector are Entrez gene IDs.

all

A vector with the Entrez IDs in the reference set. If the data was obtained from a microarray experiment,this set will contain all genes present on the specific array used for the experiment.This vector should contain all names of the de argument.

organism

A three letter character designating the organism. See a full list at ftp://ftp.genome.jp/pub/kegg/xml/organisms.

data.dir

Location of the "organism"SPIA.RData file containing the pathways data .If set to NULL will look for this file in the extdata folder of the PMAPscore library.

pathids

A character vector with the names of the pathways to be analyzed.If left NULL all pathways available will be tested.

verbose

If set to TRUE, displays the number of pathways already analyzed.

beta

Weights to be assigned to each type of gene/protein relation type. It should be a named numeric vector of length 23, whose names must be: c("activation","compound","binding/association","expression", "inhibition","activation_phosphorylation","phosphorylation", "indirect","inhibition_phosphorylation","dephosphorylation_inhibition", "dissociation","dephosphorylation","activation_dephosphorylation", "state","activation_indirect","inhibition_ubiquination","ubiquination", "expression_indirect","indirect_inhibition","repression", "binding/association_phosphorylation","dissociation_phosphorylation","indirect_phosphorylation") If set to null, beta will be by default chosen as: c(1,0,0,1,1,1,0,0,1,1,0,0,1,0,1,1,0,1,1,1,0,0,0).

Value

Get one Data in data frame format,which cotains pathway's id,pathway's name and PFS_score.