Use of PFAM.db and select function

Question

[l.willianpacheco]

Hi everyone

I'm trying to use the select() function with the PFAM.db package but I'm not succeeding.

> library("PFAM.db")
> columns(PFAM.db)
#Error in (function (classes, fdef, mtable)  : 
#    unable to find an inherited method for function ‘columns’ for signature ‘"data.frame"’
> keytypes(PFAM.db)
#Error in (function (classes, fdef, mtable)  : 
#    unable to find an inherited method for function ‘columns’ for signature ‘"data.frame"’

Just the ls() function return results, but I don't know how to use it in select()

> ls("package:PFAM.db")
# [1] "PFAM"                  "PFAM_dbconn"           "PFAM_dbfile"           "PFAM_dbInfo"          
# [5] "PFAM_dbschema"         "PFAMCAZY"              "PFAMCAZY2AC"           "PFAMDE"               
# [9] "PFAMDE2AC"             "PFAMHOMSTRAD"          "PFAMHOMSTRAD2AC"       "PFAMID"               
#[13] "PFAMID2AC"             "PFAMINTERPRO"          "PFAMINTERPRO2AC"       "PFAMLOAD"             
#[17] "PFAMLOAD2AC"           "PFAMMAPCOUNTS"         "PFAMMEROPS"            "PFAMMEROPS2AC"        
#[21] "PFAMMIM"               "PFAMMIM2AC"            "PFAMPDB"               "PFAMPDB2AC"           
#[25] "PFAMPRINTS"            "PFAMPRINTS2AC"         "PFAMPROSITE"           "PFAMPROSITE2AC"       
#[29] "PFAMPROSITEPROFILE"    "PFAMPROSITEPROFILE2AC" "PFAMRM"                "PFAMRM2AC"            
#[33] "PFAMSCOP"              "PFAMSCOP2AC"           "PFAMSMART"             "PFAMSMART2AC"         
#[37] "PFAMTC"                "PFAMTC2AC"             "PFAMTP"                "PFAMTP2AC"            
#[41] "PFAMURL"               "PFAMURL2AC"           

> PFAM.2<-select(PFAM.db, keys=keys(PFAM.db, keytypes=c("PFAMID")), columns=c("PFAMPDB", "PFAMINTERPRO"),  keytype="PFAMID")
#Error in (function (classes, fdef, mtable)  : 
#  unable to find an inherited method for function ‘select’ for signature ‘"data.frame"’

Is there anyone that knows how to use the select() function with PFAM.db package?

Thanks!

Answer 1

[mikroevdenevenakliyat]

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