View source: R/differential_expression.R
DE_analyze | R Documentation |
This function runs DE analysis on a count matrix (DESeq) or a normalized log or log-CPM matrix (limma) contained in the se object
DE_analyze(se, method, batch, conditions, assay_to_analyze)
se |
SummarizedExperiment object |
method |
DE analysis method option (either 'DESeq2' or 'limma') |
batch |
metadata column in the se object representing batch |
conditions |
metadata columns in the se object representing additional analysis covariates |
assay_to_analyze |
Assay in the se object (either counts for DESeq2 or normalized data for limma) for DE analysis |
A named list containing the log2FoldChange, pvalue and adjusted pvalue (padj) for each analysis returned by DESeq2 or limma
library(scran)
se <- mockSCE()
differential_expression <- BatchQC::DE_analyze(se = se,
method = "DESeq2",
batch = "Treatment",
conditions = c(
"Mutation_Status"),
assay_to_analyze = "counts")
pval_summary(differential_expression)
pval_plotter(differential_expression)
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