Hello Anestis,
Character encoding is really a big headache in R while on Windows. Write in your terminal :
library(readr)
locale()
and check the encoding in the output. If it says UTF-8 then your data are written in another encoding. Symbols for characters means that you are telling R to read data in e.g. UTF-8 encoding and actually data contain characters in another encoding. So you must know the encoding of your data and read them setting the locale properties to match encodings. UTF-8 should do the job.
You can also use the read.table function from base R.
read.table("data.tsv, sep = '\t', header = TRUE, encoding = "UTF-8")
if this isn't working for your data, open the file with Libre Calc and export them as a csv using UTF-8 encoding and then try to read it.
You must know that on Windows, R and encoding have problems. Try to be sure that your data are always in UTF-8 encoding. I personally prefer to do all the job on my Linux platform, save it as RData for example and then everything on Windows with a UTF-8 locale encoding is working like a charm.
I hope this is helpful. I'm a Greek too and this is really a big problem.