Description Usage Arguments Value
Function to perform entire limma+voom analysis using voom with quality weights, and beginning with a SummarizedExperiment and ending with list of differential genes and generation of diagnostic plots along the way.
1 2 3 | limma_pipe(se = NULL, design = NULL, contrast = NULL,
block.column = NULL, norm.method = "TMM", adjust.method = "BH",
p.value = 0.05)
|
se |
SummarizedExperiment with an assay slot named counts_fil containing the filtered counts and colData slot containing sample metadata. |
design |
A design matrix specifying the experimental design. If NULL, then a design matrix will be created using the values for contrast.levels and block.levels. |
contrast |
A matrix of contrasts (as created by |
block.column |
The column in the samples metadata dataframe specifying the block/additive effect column. Ignored if design is not NULL. |
norm.method |
Normalisation method to use - may be "TMM", "RLE", "upperquartile" or "none". |
adjust.method |
Method to be used for adjustment of nominal p-values. May be one of "BH", "bonferroni", "holm", "hochberg", "hommel", "BY". |
p.value |
Value between 0 and 1. Adjusted p-value for the differential expression analysis. |
Results of limma+voom differential analysis.
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