MAvalues: Create values (M and A) for MA plot

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

Create values (M and A) for MA plot

Description

The function MAvalues will create MA values as input for the function MAplot and hoeffDValues. M and A are specified relative to specified samples which is determined by the group argument. In case of group == "all", all samples (expect the specified one) are taken for the reference calculation. In case of group != "all" will use the samples belonging to the same group given in colnames(colData(se)) expect the specified one.

Usage

MAvalues(se, log2 = TRUE, group = c("all", colnames(colData(se))))

Arguments

se	SummarizedExperiment
log2	logical, specifies if values are log2-transformed prior to calculating M and A values. If the values are already transformed, log2 should be set to FALSE. If log2 = TRUE and if there are values in assay(se) that are 0, the log2 values are calculated by log2(assay(se) + 1)
group	character, either "all" or one of colnames(colData(se))

Value

tbl with columns Feature, name (sample name), A, M and additional columns of colData(se)

Examples

## create se
set.seed(1)
a <- matrix(rnorm(10000), nrow = 1000, ncol = 10, 
            dimnames = list(seq_len(1000), paste("sample", seq_len(10))))
a[c(1, 5, 8), seq_len(5)] <- NA
cD <- data.frame(name = colnames(a), type = c(rep("1", 5), rep("2", 5)))
rD <- data.frame(spectra = rownames(a))
se <- SummarizedExperiment(assay = a, rowData = rD, colData = cD)

MAvalues(se, log = FALSE, group = "all")

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