Read single-cell proteomics tabular data

Function to import and convert tabular data from a spreadsheet or a data.frame into a SingleCellExperiment and QFeatures object.

Usage

readSCP(..., experimentsAsSce = FALSE)

readSCPfromDIANN(..., experimentsAsSce = FALSE)

readSingleCellExperiment(...)

Arguments

...

Parameters passed to readSummarizedExperiment(), readQFeatures() or readQFeaturesFromDIANN(). See these respective manual pages for details.

experimentsAsSce

A logical(1) indicating whether the QFeatures object should be composed of SingleCellExperiment objects. By default: FALSE, the QFeatures object will be composed of SummarizedExperiment objects. Note that using SingleCellExperiment can impact the performance.

Value

An instance of class SingleCellExperiment or a QFeatures, composed of SingleCellExperiment or SummarizedExperiment objects.

Note

The SingleCellExperiment class is built on top of the RangedSummarizedExperiment class. This means that some column names are forbidden in the rowData. Avoid using the following names: seqnames, ranges, strand, start, end, width, element

See also

• The more general QFeatures::readQFeatures() function, which this function depends on.

• The more general QFeatures::readQFeaturesFromDIANN() function, for details and an example on how to read label-free and plexDIA (mTRAQ) data processed with DIA-NN.

• The QFeatures::readSummarizedExperiment() function, which readSingleCellExperiment() depends on.

• The SingleCellExperiment::SingleCellExperiment() class.

Examples

######################################################
## Load a single acquisition as a SingleCellExperiment

## Load a data.frame with PSM-level data
data("mqScpData")

## Create the QFeatures object
quantCols <- grep("Reporter.intensity.\\d", colnames(mqScpData))
sce <- readSingleCellExperiment(mqScpData, quantCols)
sce
#> class: SingleCellExperiment 
#> dim: 1361 16 
#> metadata(0):
#> assays(1): ''
#> rownames(1361): 1 2 ... 1360 1361
#> rowData names(133): uid Sequence ... residual participated
#> colnames(16): Reporter.intensity.1 Reporter.intensity.2 ...
#>   Reporter.intensity.15 Reporter.intensity.16
#> colData names(0):
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):

######################################################
## Load multiple acquisitions as a QFeatures

## Load an example table containing MaxQuant output
data("mqScpData")

## Load the (user-generated) annotation table
data("sampleAnnotation")

## Format the tables into a QFeatures object
readSCP(assayData = mqScpData,
        colData = sampleAnnotation,
        runCol = "Raw.file")
#> Checking arguments.
#> Loading data as a 'SummarizedExperiment' object.
#> Splitting data in runs.
#> 
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#> Formatting sample annotations (colData).
#> Formatting data as a 'QFeatures' object.
#> An instance of class QFeatures (type: scp) with 4 sets:
#> 
#>  [1] 190222S_LCA9_X_FP94BM: SummarizedExperiment with 395 rows and 16 columns 
#>  [2] 190321S_LCA10_X_FP97AG: SummarizedExperiment with 487 rows and 16 columns 
#>  [3] 190321S_LCA10_X_FP97_blank_01: SummarizedExperiment with 109 rows and 16 columns 
#>  [4] 190914S_LCB3_X_16plex_Set_21: SummarizedExperiment with 370 rows and 16 columns