Yes! Thank You, Emmanuel!
This works perfectly. In same way I edited also del.rowgapsonly()
Sincerely,
V.
Dne úterý 2. listopadu 2021 15:12:47 CET, Emmanuel Paradis napsal(a):
> Ha! That's because gaps are coded with dashes in your files; I assumed
> it was X's (as returned by ape::trans). So
Ha! That's because gaps are coded with dashes in your files; I assumed it was
X's (as returned by ape::trans). So this line 7 should be:
foo <- function(x) sum(x == 0x58 | x == 0x2d)
Or (probably easier to modify):
foo <- function(x) sum(x == charToRaw("X") | x == charToRaw("-"))
Thank You, Emmanuel,
I thought I must do something with line 7, but I had no idea what. :-)
Unfortunately it didn't work. I still get "All sequences of the same length:
249" after running the edited function as 'aln.ng <- del.colgapsonly(x=aln,
threshold=0.25, freq.only=FALSE)'... :-( I'm
Hello,
thank You, but it seems that trimEnds() requires DNAbin. I checked also other
functions from ips, and it seems to be the same...
Sincerely,
V.
Dne úterý 2. listopadu 2021 12:13:06 CET jste napsal(a):
> Dear Vojtech,
> Did you check this https://rdrr.io/cran/ips/man/trimEnds.html
> Franz
>
Hi Vojtěch,
In addition to removing lines 3 and 4, replace line 7:
foo <- function(x) sum(x == 4)
by:
foo <- function(x) sum(x == 0x58)
That sh(c)ould do it.
Best,
Emmanuel
- Le 2 Nov 21, à 17:37, Vojtěch Zeisek vo...@trapa.cz a écrit :
> Hello,
> I try to trim protein
Hello,
I try to trim protein alignments in R. I see del.colgapsonly() and
del.rowgapsonly() from ape can trim only class DNAbin. As DNAbin as basically
same matrix as AAbin (Isn't it?), I thought it should be easy. I commented out
lines 3 and 4 in both del.colgapsonly() and del.rowgapsonly(),
