msea_ora: MSEA by over representation analysis

Description Usage Arguments Value Author(s) References Examples

View source: R/msea_ora.R

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

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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

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	# -----------------------
	#  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.