measured_category {MatrixQCvis}

R Documentation

Obtain the number of measured intensities per sample type

Description

The function 'measured_category' creates a 'tbl' with the number of measured values per feature. 0 means that there were only missing values ('NA') for the feature and sample type. 'measured_category' will return a 'tbl' where columns are the unique sample types and rows are the features as in 'assay(se)'.

Usage

measured_category(se, measured = TRUE, category = "type")

Arguments

se	'SummarizedExperiment'
measured	'logical', should the measured values ('measured = TRUE') or missing values ('measured = FALSE') be taken
category	'character', corresponds to a column name in 'colData(se)'

Details

'measured_category' is a helper function.

Value

'tbl' with number of measured/mising features per 'category' type

Examples

## create se
set.seed(1)
a <- matrix(rnorm(100), nrow = 10, ncol = 10,
            dimnames = list(1:10, paste("sample", 1:10)))
a[c(1, 5, 8), 1:5] <- NA
cD <- data.frame(name = colnames(a), type = c(rep("1", 5), rep("2", 5)))
rD <- data.frame(spectra = rownames(a))
se <- SummarizedExperiment::SummarizedExperiment(assay = a,
    rowData = rD, colData = cD)

measured_category(se, measured = TRUE, category = "type")

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