shinyQC: Shiny application for initial QC exploration of -omics data...

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

Shiny application for initial QC exploration of -omics data sets

Description

The shiny application allows to explore -omics data sets especially with a focus on quality control. shinyQC gives information on the type of samples included (if this was previously specified within the SummarizedExperiment object). It gives information on the number of missing and measured values across features and across sets (e.g. quality control samples, control, and treatment groups, only displayed for SummarizedExperiment objects that contain missing values).

shinyQC includes functionality to display (count/intensity) values across samples (to detect drifts in intensity values during the measurement), to display mean-sd plots, MA plots, ECDF plots, and distance plots between samples. shinyQC includes functionality to perform dimensionality reduction (currently limited to PCA, PCoA, NMDS, tSNE, and UMAP). Additionally, it includes functionality to perform differential expression analysis (currently limited to moderated t-tests and the Wald test).

Usage

shinyQC(se, app_server = FALSE)

Arguments

se	SummarizedExperiment object (can be omitted)
app_server	logical (set to TRUE if run under a server environment)

Details

rownames(se) should be set to the corresponding name of features, while colnames(se) should be set to the sample IDs. rownames(se) and colnames(se) are not allowed to be NULL. colnames(se), colnames(assay(se)) and rownames(colData(se)) all have to be identical.

shinyQC allows to subset the supplied SummarizedExperiment object.

On exit of the shiny application, the (subsetted) SummarizedExperiment object is returned with information on the processing steps (normalization, transformation, batch correction and imputation). The object will only returned if app_server = FALSE and if the function call is assigned to an object, e.g. tmp <- shinyQC(se).

If the se argument is omitted the app will load an interface that allows for data upload.

Value

shiny application, SummarizedExperiment upon exiting the shiny application

Author(s)

Thomas Naake

Examples

library(dplyr)
library(SummarizedExperiment)

## create se
set.seed(1)
a <- matrix(rnorm(100, mean = 10, sd = 2), nrow = 10, ncol = 10, 
            dimnames = list(seq_len(10), 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)

shinyQC(se)

tnaake/MatrixQCvis documentation built on June 20, 2024, 7:22 a.m.