Description Usage Arguments Value
Function to perform entire DESeq2 analysis, beginning with a SummarizedExperiment and ending with list of differential genes and generation of diagnostic plots along the way.
1 2 | deseq2_pipe(se = NULL, block.column = NULL, 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. |
block.column |
The column in the samples metadata dataframe specifying the block/additive effect column. |
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. |
List containing the DESeq2 DDS container, the raw results for each contrast and the processed differential gene results.
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