Error parsing "complex" contrast names

[TobiTekath]

Hi Constantin,

I just came across an error in the handling of contrast names in test_de(). The error appears when using a model.matrix with "complex" names (see below)

Code to reproduce:

library(glmGamPoi)
Y <- matrix(rnbinom(n = 30 * 100, mu = 4, size = 0.3), nrow = 30, ncol = 100)
annot <- data.frame(sample = sample(LETTERS[1:6], size = 100, replace = TRUE),
                    grp = sample(LETTERS[1:2], size = 100, replace = TRUE))
se <- SummarizedExperiment::SummarizedExperiment(Y, colData = annot)
mm <- model.matrix(~annot$grp)
fit <- glm_gp(se, design = mm)
test_de(fit, contrast = "annot$grpB")

Error:

 Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x),  : 
  'data' must be of a vector type, was 'NULL'

I traced the Error to https://github.com/const-ae/glmGamPoi/blob/b595fd7fbdba98a89ca57dbcbb38baa151e4c767/R/parse_contrast.R#L38 which returns NULL in this context (and not the correct column name as supposed).

The error can be circumvented by defining the model.matrix more elegantly (model.matrix(~grp, annot)), but as the matrices themselves are identical (except for the column names), I still think this might be an error you want to catch.

Best, Tobi

[const-ae]

Hi Tobi,

thanks for the report and the detailed description which made it easy to understand what is happening. The easiest way to avoid that error is actually to use

test_de(fit, contrast = "`annot$grpB`")

Note the ticks ` around annot$grpB. This is necessary to make sure that the contrast is indeed interpretated as a name and not some R expression.

I am not sure that this is a problem that I would be able to detect in parse_contrast. However, if you have a suggestion to provide a more meaningful error message, I would be happy to hear :)

[TobiTekath]

Hi Constantin,

thank you for the immediate feedback. You are absolutely right, the backticks are a very elegant way to prevent evaluation. Thanks.