I am trying to normalize my raw methylation beta-values using minfi with R version 3.6.0. I have been following the bioconductor user guide in order to do so:
After running the preprocessQuantile function, I receive the following standard messages:
# [preprocessQuantile] Mapping to genome. # [preprocessQuantile] Fixing outliers. # [preprocessQuantile] Quantile normalizing.
As well as the following warning message:
# Warning message: # In .getSex(CN = CN, xIndex = xIndex, yIndex = yIndex, cutoff = cutoff) : An inconsistency was encountered while determining sex. One possibility is that only one sex is present. We recommend further checks, for example with the plotSex function.
I am not concerned about the warning message because I do expect for all my samples to be female.
My issue is with exporting the preprocessQuantile normalized beta values from R. The Bioconductor Minfi User Guide states that: "Note: The function returns a GenomicRatioSet object ready for downstream analysis."
I tried using write.table function to do so and received this error:
# Error in as.vector(x) : no method for coercing this S4 class to a vector.
Is it not possible to export files into .txt format?
For reference also, this is the write.table function that I had used:
write.table(GRset_ascites.quantile, "H:/Cyto/PCPGM/IDAT/Cytoquantilenorm.txt", sep="\t")
I am admittedly inexperienced with R, but still learning! I'm also a long-time-lurker on Biostars, but this is my first time posting so please critique my question as needed. :)