printGraph: Print the results of identification

Description

Print the identification results of MPINet.

Usage

printGraph(ann,detail=FALSE,method="MPINet",pathType="KEGG")

Arguments

ann

A list. The results returned from the function identifypathway.

detail

A logical. If true, metabolite lists from the function identifypathway are converted into strings, which are used to display and write results with metabolites.

method

A character string. which is the argument method used in the function identifypathway.

pathType

A character string vector. which is the argument pathType used in the function identifypathway.

Value

A data.frame of the identification results. (i)If the argument method is "MPINet", it includes the following elements: 'pathwayName', 'annComponentRatio', 'annBgRatio', 'weight', 'pvalue', 'fdr', 'annComponentList', 'annBgComponentList', 'annComponentinNetRatio', 'anncompinNetworkList', 'riskcompinNetworkList'. The 'annComponentRatio' is the ratio of the annotated metabolites. For example, 30/1000 means that 30 metabolites in 1000 interesting metabolites are annotated in this pathway. The 'annBgRatio' is the ratio of background metabolites, for example, 10/4994 means that 10 of the 4994 human metabolites in the background are annotated in this pathway. The 'annComponentinNetRatio' indicates the ratio of annotated metabolites in the global human metabolite network. The 'annComponentList' and 'annBgComponentList' are the annotated metabolites and the annotated background metabolites. The 'anncompinNetworkList' and 'riskcompinNetworkList' are the annotated metabolites in network and the interesting metabolites in network. (ii)If the argument method is "Hyper", it includes the following elements: 'pathwayName', 'annComponentRatio', 'annBgRatio', 'pvalue', 'fdr', 'annComponentList', 'annBgComponentList'. When the argument pathType is "KEGG", the 'pathwayID' is included. When the the argument pathType is not "KEGG", the 'pathsource' is included. Detailed information is provided in the function identifypathway.

Details

The function can convert the results of identification to data.frame.

Note that the argument method and pathType should be assigned the same as the function identifypathway.

Examples

Run this code

## Not run: 
# 
# #######################################
# 
# #get example data
# #### get the type 2 diabetes data set 1
# risk<-GetExampleData(dataset="diabetes1") 
# #### integrate the non-equivalence of metabolites and the character of
# #### differential metabolites by the monotonic spline model 
# pss<-getPSS(risk,plot=TRUE)         
# #identify dysregulated pathways
# anncpdpre<-identifypathway(risk,pss,pathType="KEGG",method="MPINet",annlim=1,bglim=6)
# #convert ann to data.frame
# result<-printGraph(anncpdpre,pathType="KEGG",method="MPINet")
# #print part of the results to screen
# head(result)
# 
# result1<-printGraph(anncpdpre,pathType="KEGG",method="MPINet",detail=TRUE)
# #print part of the results to screen
# head(result1)
# 
# 
# 
# 
# 
# 
# ## End(Not run)