variableGenes {MetaNeighbor} | R Documentation |
Identifies genes with high variance compared to their median expression (top quartile) within each experimentCertain function
variableGenes( dat, i = 1, exp_labels, min_recurrence = length(unique(exp_labels)), downsampling_size = 10000 )
dat |
SummarizedExperiment object containing gene-by-sample expression matrix. |
i |
default value 1; non-zero index value of assay containing the matrix data |
exp_labels |
character vector that denotes the source (Study ID) of each sample. |
min_recurrence |
Number of studies across which a gene must be detected as highly variable to be kept. By default, only genes that are variable across all studies are kept (intersection). |
downsampling_size |
Downsample each study to downsampling_size samples without replacement. If set to 0 or value exceeds dataset size, no downsampling is applied. |
The output is a vector of gene names that are highly variable in every experiment (intersect)
data(mn_data) var_genes = variableGenes(dat = mn_data, exp_labels = mn_data$study_id) var_genes