getMetabolites: Loads and/or subsets metabolite data.

In buddha2490/BERGMets: Metabolomics data and analysis in the BERG

Description

Each metabolomics dataset has multiple versions based on how the lab chose to scale them. This function will pull the correct data.

Usage

getMetabolites(dat, IDlist=NULL, compid=NULL)

Arguments

dat	Character vector of the dataset you are requesting (see details below). Options are NOT case sensitive.
IDlist	Optional: Character vector of a subset of IDs. If you have already prepared your covariate dataset, you can include a vector of IDs for subsetting the metabolite data. If you leave it NULL, all data will be returned.
compid	Optional: Character vector of a subset of COMP_IDs. If you know what metabolites you are looking for, you can enter a vector of these COMP_IDs and only pull these data.

Details

Users can pull data from any of 7 metabolomics projects using the following character strings. For more information, you can find documentation by searching the BERGMets documentation:

1. "breast_metabolomics"

2. "Parkinsons_C8"

3. "Parkinsons_HILICNEG"

4. "Parkinsons_HILICPOS"

5. "prostate_metabolomics"

6. "Validation_Blood"

7. "Validation_Urine"

Value

getMetabolites will return a list of 3 objects:

$metabolites - Data frame of the metabolite data organized by ID

$ID - and ID conversion file, useful if you need to pull lifelink data or refer to the original data files

$biochem - Biochemical metadata: includes biochemical names, pathway information, platform/batch information, QC metrics (CV, ICC, N-missing, etc)

Author(s)

Brian Carter

Examples

# Access documentation for the breast_metabolomics file:

?breast_metabolomics

# Pull all data

breast_metabolites <- getMetabolites("breast_metabolomics")

names(breast_metabolites)

# Pull just some IDs

ID <- c("42101011001022",
        "55010005007081",
        "43017011009062",
        "56017043004052",
        "06026241020062")

breast_metabolites <- getMetabolites("breast_metabolomics", IDlist=ID)

nrow(breast_metabolites$metabolites)

# Pull just some metabolites

mets <- c("X34404","X21132",
          "X57463","X37183",
          "X39346")

breast_metabolites <- getMetabolites("breast_metabolomics", compid=mets)

ncol(breast$metabolites$metabolites)

# Pull just some metabolites for just some IDs

breast_metabolites <- getMetabolites("breast_metabolomics",
                                     IDlist=ID, =compid=mets)

dim(breast_metabolites$metabolites)

buddha2490/BERGMets documentation built on Sept. 6, 2020, 5:11 p.m.