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?
Do you mean the description here in the lncDIFF topic is not enough ?
Please use comments to request more details/clarification. Answers must answer the question.
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)
Note that the first level alphabetically is treated as the reference group in R.
In this case, R is taking control as reference.
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