Package lncDIFF input files format
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8 weeks ago
valopes ▴ 30

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?

RNA-Seq Tool • 141 views
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Hi, Do you mean the description here in the lncDIFF topic is not enough ?

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

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8 weeks ago

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)
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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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