MTBLS79 {pmp} | R Documentation

## Direct-infusion mass spectrometry (DIMS) data set

### Description

Data set of 20 biological (cow vs sheep) serum samples that were analysed repeatedly, in 8 batches across 7 days.

### Usage

    MTBLS79

### Format

A RangedSummarizedExperiment-class object.
`assay(MTBLS79)` Peak intensities of the DIMS data set. Contains 172 samples and 2488 features.
`colData(MTBLS79)` Sample meta data containing 4 columns.
`Batch` - `character()`, sample batch name.
`Sample_Rep` - `character()`, sample replicate code.
`Class` - `character()`, sample class labels.
`Class2` - `character()`, alternative sample class labels grouping together replicate samples.

### Details

Code below includes all commands used to generate MTBLS79 object.

    library (openxlsx)
    library (SummarizedExperiment)

    download.file(destfile = "MTBLS79.xlsx", mode="wb",
    url = "ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/
       MTBLS79/Dataset07__SFPM.xlsx")
    wb <- openxlsx::loadWorkbook(xlsxFile="MTBLS79.xlsx")

    MTBLS79 <- list()

    MTBLS79$assay <- openxlsx::readWorkbook(wb, "data", colNames=T, rowNames=T)

    # Last row of the peak matrix represent mean intensities across all samples.
    MTBLS79$assay <- MTBLS79$assay[-c(nrow(MTBLS79$assay)), ]

    # Transpose peak matrix, so that features are in rows and samples in columns.
    MTBLS79$assay <- as.matrix(t(MTBLS79$assay))

    # Missing values in the input data are stored as 0, replace with NA
    MTBLS79$assay[MTBLS79$assay == 0] <- NA

    rownames(MTBLS79$assay) <- round(as.numeric(rownames(MTBLS79$assay)), 5)

    MTBLS79$colData <- openxlsx::readWorkbook(wb, "meta", colNames=T, rowNames=F)
    MTBLS79$colData <- MTBLS79$colData[-c(nrow(MTBLS79$colData)), 1:4]

    MTBLS79 <- SummarizedExperiment(assays=list(MTBLS79$assay),
    colData=DataFrame(MTBLS79$colData))

### Source

https://www.ebi.ac.uk/metabolights/MTBLS79

### References

Kirwan et al, Scientific Data volume 1, Article number: 140012 (2014) https://www.nature.com/articles/sdata201412

[Package pmp version 1.4.0 Index]