h_diff_expr_deseq2 | R Documentation |
This helper functions performs the differential expression analysis with
DESeq2::DESeq()
for a given AnyHermesData input and design
matrix.
h_diff_expr_deseq2(object, design, ...)
object |
( |
design |
( |
... |
additional arguments internally passed to |
A data frame with columns log2_fc
(estimated log2 fold change),
stat
(Wald statistic), p_val
(raw p-value), adj_p_pval
(Benjamini-Hochberg adjusted p-value).
DESeq2_packagehermes
object <- hermes_data # Create the design matrix corresponding to the factor of interest. design <- model.matrix(~SEX, colData(object)) # Then perform the `DESeq2` differential expression analysis. result <- h_diff_expr_deseq2(object, design) head(result) # Change of the `fitType` can be required in some cases. result2 <- h_diff_expr_deseq2(object, design, fitType = "local") head(result2)
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