msea_ora: MSEA by over representation analysis

In mseapca: Metabolite set enrichment analysis for factor loading in principal component analysis

Description

This function performs metabolite set enrichment analysis by over representation analysis (ORA). Statistical hypothesis test of cross tabulation is performed by one-sided Fisher's exact test.

Usage

msea_ora(SIG, ALL, M)

Arguments

SIG	Metabolite IDs of significant metabolites
ALL	Metabolite IDs of all detected metabolites
M	list of metabolite set name and metabolite IDs

Value

list of p-value and q-value for metabolite set and selected (significant) metabolite IDs for each metabolite set

Author(s)

Hiroyuki Yamamoto

References

Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA. Global functional profiling of gene expression. Genomics. 2003 Feb;81(2):98-104.

Examples

	# -----------------------
	#  load metabolite set
	# -----------------------
	# filename <- "C:/pathway.xml"
	# M <- read_pathway(filename) 		# load metabolite set list
	
	# ----------------------
	#  Set metabolite IDs
	# ----------------------
	## p : dataframe of metabolite IDs and p-value of factor loadings in PCA
	## fl : dataframe of metabolite IDs and factor loadings in PCA

	# ALL <- p[,1]				# All metabolite IDs
	# SIG <- p[p[,2] < 0.05 & fl[,2]<0,1] 
            ## negatively significant metabolites selected by factor loading

	# ---------------
	#  MSEA by ORA
	# ---------------
	# B <- msea_ora (SIG, ALL, M)

Example output

Loading required package: XML

mseapca documentation built on May 29, 2017, 9:49 a.m.