topDirs function isn't compatible with hic_glm when multiple contrasts are passed through

[serine]

Hi @mdozmorov ,

I'm not 100%, but it looks like topDirs function isn't compatible with hic_glm if I pass multiple contrasts.

design <- model.matrix(~0+groups)
colnames(design) <- gsub("groups", "", colnames(design))
rownames(design) <- meta$samples

contrasts <- limma::makeContrasts(mock1_vs_mock2=mock2-mock1,
                                  mock3_vs_mock4=mock4-mock3,
                                  levels = design)

hic_fit <- hic_glm(hic_exp,
                   design = design,
                   contrast = contrasts,
                   method = "QLFTest",
                   p.method = "fdr",
                   parallel = TRUE)

when I call results(hic_fit) I get nice table with all contrasts tested, but the columns labeled like this logFC.mock1_vs_mock2 and logFC.mock3_vs_mock4. From what I can tell topDirs expects logFC column label here

It isn't an issue for me, I can workaround by just using results function, but I thought it would be worth raising for future improvements.

Thanks,

[mdozmorov]

Indeed, working with multiple contrasts would be good to implement. We haven't tested it that thoroughly. I'll keep this issue open, or @serine, please, make a pull request if you fix it.