Hi,

How is it with the bamCount function - does it still have option paired.end="extend"? What does it mean when paired.end="filter" (it is not written in the documentation of the function)?

> bamsignals_bamCount=bamsignals::bamCount(signal1, windows, verbose=FALSE, paired.end="extend")
Błąd w poleceniu 'match.arg(paired.end)':
  'arg' should be one of “ignore”, “filter”, “midpoint”

Thanks,  Kasia

Hi Kasia,

thanks for your question and sorry for answering only now (I didn't get any notification...).

That's correct, the bamCount function does not have the option paired.end="extend". It wouldn't make sense, because bamCount counts the 5' end of a read, so if you extend it to the whole fragment the 5' end actually does not change. 

This is what the docs say about the "filter" option:

If ‘paired.end!="ignore"’ then only first reads in proper mapped pairs will be consider (i.e. in the flag of the  read, the bits in the mask 66 must be all ones)

so when you set paired.end="filter", only one read per pair will be counted (the first in the pair).

Let me know if I can help!

Alessandro