Package lncDIFF input files format

Question

[valopes]

Hi, all!

I am trying to run Package ‘lncDIFF’ in R. However, the description of file formats is so poor.

I need a better description for the all required files: edata, group, covariate, and CompareGroups. Is there someone that could help me?

[Basti]

Hi, Do you mean the description here in the lncDIFF topic is not enough ?

[Ram]

Please use comments to request more details/clarification. Answers must answer the question.

Answer 1

[Cristina Zamora]

I've being working on it and it is easier than expected. Simple example, comparison between disease and control with 3 libraries each:

Data must be a data.frame of expression normalized values with genes (rows) and samples/libraries (columns). Prepare the required options:

libraries <- c("disease","disease","disease","control","control","control")
comp <- c("disease","control")

DELnc <- lncDIFF(edata= exp, 
        group = libraries, 
        covariate = NULL,
        link.function = "log",
        CompareGroups = comp,
        simulated.pvalue = FALSE,
        permutation = 100)

table(DELnc$DE.results$DE.Gene)

[Cristina Zamora]

Note that the first level alphabetically is treated as the reference group in R. In this case, R is taking control as reference.