代谢产物差异分析 | 生信菜鸟团 http://www.bio-info-trainee.com/8512.html

MetaboSignal2.knit

使用MetaboDiff包分析非靶向代谢组数据 - 简书最近手里有个非靶向代谢组的数据，通过学习MetaboDiff包来熟悉代谢组分析的思路和流程，接下来的流程来自于MetaboDiff包官方帮助文档。 1. MetaboDiff...https://www.jianshu.com/p/80af83c2f630https://www.metaboanalyst.ca/docs/RTutorial.xhtmlhttps://www.metaboanalyst.ca/docs/RTutorial.xhtmlhttps://www.metaboanalyst.ca/docs/APIs.xhtml

物尽其用｜最全的HMDB数据库使用教程在这里

    The different options for input.type are given below:name - Compound name (e.g., 1,3-Diaminopropane)hmdb - Human Metabolome Database (e.g., HMDB0000002)pubchem - PubChem Substance and Compound databases(e.g., 428)chebi - Chemical Entities of Biological Interest(e.g., 15725)metlin - Metabolite and Chemical Entity Database (e.g., 5081)kegg - KEGG COMPOUND Database (e.g., C00986)

https://drive.google.com/file/d/1bLHQC8G7n9XyBG4Vim63hhICb4Qtw36M/viewhttps://drive.google.com/file/d/1bLHQC8G7n9XyBG4Vim63hhICb4Qtw36M/view

2.1 Over representation analysis
We will go over two analysis workflows, the first is when the input is a list to perform over representation

analysis. The first step is to create a vector containing a list of compound names. The list will then be cross-
referenced (CrossReferencing) against the MetaboAnalyst compound libraries (HMDB, PubChem, KEGG,

etc.), and any compounds without a hit will have NA. This step may take long due to downloading of libraries
if they do not already exist in your working directory.

InitDataObjects {MetaboAnalystR}

R Documentation

Constructs a dataSet object for storing data

Description

This functions handles the construction of a mSetObj object for storing data for further processing and analysis. It is necessary to utilize this function to specify to MetaboAnalystR the type of data and the type of analysis you will perform.

Usage

InitDataObjects(data.type, anal.type, paired=FALSE)

Arguments

data.type	The type of data, either list (Compound lists), conc (Compound concentration data), specbin (Binned spectra data), pktable (Peak intensity table), nmrpeak (NMR peak lists), mspeak (MS peak lists), or msspec (MS spectra data)
anal.type	Indicate the analysis module to be performed: stat, pathora, pathqea, msetora, msetssp, msetqea, mf, cmpdmap, smpmap, or pathinteg
paired	Indicate if the data is paired or not. Logical, default set to FALSE

Author(s)

Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)

==============================

CreateMappingResultTable {MetaboAnalystR}

R Documentation

Creates the mapping result table

Description

Creates the mapping result table

Usage

CreateMappingResultTable(mSetObj = NA)

Arguments

mSetObj

Input the name of the created mSetObj (see InitDataObjects)

---

[Package MetaboAnalystR version 4.0.0 Index]

---------------==============================================

CrossReferencing {MetaboAnalystR}

R Documentation

Various functions for mapping b/w names & database identifiers Given a list of compound names or ids, find matched name or ids from selected databases

Description

Given a list of compound names or ids find matched name or IDs from selected databases

Usage

CrossReferencing(mSetObj = NA,q.type,hmdb = T,pubchem = T,chebi = F,kegg = T,metlin = F,lipid = F
)

Arguments

mSetObj	Input the name of the created mSetObj (see InitDataObjects).
q.type	Input the query type, "name" for compound names, "hmdb" for HMDB IDs, "kegg" for KEGG IDs, "pubchem" for PubChem CIDs, "chebi" for ChEBI IDs, "metlin" for METLIN IDs, and "hmdb_kegg" for a both KEGG and HMDB IDs.
hmdb	Logical, T to cross reference to HMDB, F to not.
pubchem	Logical, T to cross reference to PubChem, F to not.
chebi	Logical, T to cross reference to CheBI, F to not.
kegg	Logical, T to cross reference to KEGG, F to not.
metlin	Logical, T to cross reference to MetLin, F to not.
lipid	Logical, if features are lipids (T), a different database will be used for compound matching.

Author(s)

Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)

========================================

PerformDetailMatch {MetaboAnalystR}

R Documentation

Perform detailed name match

Description

Given a query, perform compound matching.

Usage

PerformDetailMatch(mSetObj = NA, q)

Arguments

mSetObj	Input name of the created mSet Object.
q	Input the query.

===================

SetCandidate {MetaboAnalystR}

R Documentation

Set matched name based on user selection from all potential hits

Description

Note: to change object in the enclosing enviroment, use "<<-"

Usage

SetCandidate(mSetObj = NA, query_nm, can_nm)

Arguments

mSetObj	Input the name of the created mSetObj (see InitDataObjects).
query_nm	Input the query name.
can_nm	Input the candidate name.

Author(s)

Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)

 ====-------------

SetMetabolomeFilter {MetaboAnalystR}

R Documentation

Set metabolome filter

Description

Set metabolome filter

Usage

SetMetabolomeFilter(mSetObj = NA, TorF)

Arguments

mSetObj	Input the name of the created mSetObj (see InitDataObjects)
TorF	Input metabolome filter

-================

SetCurrentMsetLib {MetaboAnalystR}

R Documentation

Set current user selected metset library for search

Description

if enrichment analysis, also prepare lib by creating a list of metabolite sets

Usage

SetCurrentMsetLib(mSetObj=NA, libname, excludeNum)

Arguments

mSetObj	Input the name of the created mSetObj (see InitDataObjects)
libname	Input user selected name of library, "self", "kegg_pathway", "smpdb_pathway", "blood", "urine", "csf", "snp", "predicted", "location", and "drug".
excludeNum	Users input the mimimum number compounds within selected metabolite sets (metabolitesets < excludeNum)

Author(s)

Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL

-----------------------

CalculateHyperScore {MetaboAnalystR}

R Documentation

Over-representation analysis using hypergeometric tests

Description

Over-representation analysis using hypergeometric tests The probability is calculated from obtaining equal or higher number of hits using 1-phyper. Since phyper is a cumulative probability, to get P(X>=hit.num) => P(X>(hit.num-1))

Usage

CalculateHyperScore(mSetObj = NA)

Arguments

mSetObj

Input the name of the created mSetObj (see InitDataObjects)

Author(s)

Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)

====================

PlotORA {MetaboAnalystR}

R Documentation

Plot over-representation analysis (ORA)

Description

Plot over-representation analysis (ORA)

Usage

PlotORA(mSetObj=NA, imgName, imgOpt, format="png", dpi=72, width=NA)

Arguments

mSetObj	Input the name of the created mSetObj (see InitDataObjects)
imgName	Input a name for the plot
imgOpt	"net"
format	Select the image format, "png", or "pdf".
dpi	Input the dpi. If the image format is "pdf", users need not define the dpi. For "png" images, the default dpi is 72. It is suggested that for high-resolution images, select a dpi of 300.
width	Input the width, there are 2 default widths, the first, width = NULL, is 10.5. The second default is width = 0, where the width is 7.2. Otherwise users can input their own width.