Description Usage Arguments Author(s) Examples
View source: R/src_res_edgeR.R
Function assumes a DGEGLM object from glmQLFit and will then produce DE results based on a coef or contrast.
1 |
fit |
DGEGLM, output of glmQLFit |
contrast |
a numeric contrast so a column from edgeR::makeContrasts() |
coef |
a coefficient to test, ignored it contrast is set |
lfc |
a lfc threshold for glmTreat, if 0 falls back to glmQLTest |
ID |
the name of the column that will store the genes/regions/identifiers for each row |
Alexander Toenges
1 2 3 4 5 6 7 8 9 10 11 12 | nlibs <- 4
ngenes <- 1000
dispersion.true <- 1/rchisq(ngenes, df=10)
design <- model.matrix(~factor(c(1,1,2,2)))
y <- rnbinom(ngenes*nlibs,mu=20,size=1/dispersion.true)
y <- matrix(y,ngenes,nlibs)
rownames(y) <- paste0("Gene", seq(1,nrow(y)))
d <- DGEList(y)
d <- calcNormFactors(d)
d <- estimateDisp(d, design)
fit <- glmQLFit(d, design)
head(res_edgeR(fit=fit,coef=2))
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