extractComb: Obtain the features that are present in a specified set

In tnaake/MatrixQCvis: Shiny-based interactive data-quality exploration for omics data

Obtain the features that are present in a specified set

Description

The function extractComb extracts the features that match a combination depending if the features was measured or missing. The function will return the sets that match the combination, thus, the function might be useful when answering questions about which features are measured/missing under certain combinations (e.g. sample types or experimental conditions).

Usage

extractComb(se, combination, measured = TRUE, category = "type")

Arguments

se	SummarizedExperiment
combination	character, refers to factors in category
measured	logical
category	character, corresponding to a column name in colData(se)

Details

The function extractComb uses the make_comb_mat function from ComplexHeatmap package.

Presence is defined by a feature being measured in at least one sample of a set.

Absence is defined by a feature with only missing values (i.e. no measured values) of a set.

Value

character

Examples

## create se
a <- matrix(seq_len(100), nrow = 10, ncol = 10, 
            dimnames = list(seq_len(10), paste("sample", seq_len(10))))
a[c(1, 5, 8), seq_len(5)] <- NA
set.seed(1)
a <- a + rnorm(100)
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)

extractComb(se, combination = "2", measured = TRUE, category = "type") 

tnaake/MatrixQCvis documentation built on Nov. 4, 2024, 7:42 a.m.