degComps {DEGreport} | R Documentation |
results()
for multiple comparisonsThis function will extract the output of DESeq2::results()
and DESeq2::lfcShrink()
for multiple comparison using:
degComps( dds, combs = NULL, contrast = NULL, alpha = 0.05, skip = FALSE, type = "normal", pairs = FALSE, fdr = "default" )
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
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")