Description Usage Arguments Details Value Author(s) Examples
This function will extract the output of DESeq2::results()
and DESeq2::lfcShrink()
for multiple comparison using:
1 2 3 4 5 6 7 8 9 10 |
dds |
DESeq2::DESeqDataSet obcject. |
combs |
Optional vector indicating the coefficients or columns
fom |
contrast |
Optional vector to specify contrast. See |
alpha |
Numeric value used in independent filtering in |
skip |
Boolean to indicate whether skip shrinkage. For instance when it comes from LRT method. |
type |
Type of shrinkage estimator. See |
pairs |
Boolean to indicate whether create all comparisons or only
use the coefficient already created from |
fdr |
type of fdr correction. |
coefficients
contrast
Multiple columns in colData
that match coefficients
Multiple columns in colData
to create all possible
contrasts
DEGSet with unSrunken and Srunken results.
Lorena Pantano
1 2 3 4 5 6 7 8 9 10 | library(DESeq2)
dds <- makeExampleDESeqDataSet(betaSD=1)
colData(dds)[["treatment"]] <- sample(colData(dds)[["condition"]], 12)
design(dds) <- ~ condition + treatment
dds <- DESeq(dds)
res <- degComps(dds, combs = c("condition", 2),
contrast = list("treatment_B_vs_A", c("condition", "A", "B")))
# library(fdrtools)
#res <- degComps(dds,contrast = list("treatment_B_vs_A"),
# fdr="lfdr-stat")
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