Trim2Core2: Trim2Core2

In UriNeri/NeriMisc: Neri's Miscellaneous helper functions

Trim2Core2

Description

Misc functions for extraction of core domain region based on profile matches.

Usage

Trim2Core2(
  hits_df = Motif_df,
  faa = FL_longest_members,
  add_genetic_code = F,
  Out_faa = T,
  out_df = F,
  input_was = "new_name",
  subject_was = "profile",
  Expand_projectionX = 0
)

Arguments

hits_df	Input table (data.frame). Usually tabular search results of profile search e.g. hmmsearch
faa	Input XString/BString/DNAStringSet...
add_genetic_code	If canonical stops are identified within the core region, should this be noted in the output?
Out_faa	Should the output include the trimmed StringSet?
out_df	Should the output include the potentially modified hit table?
input_was	Column name for the input (usually seq IDs).
subject_was	Column name for the profile (usually profile IDs).
Expand_projectionX	Should the core region be expanded slightly based to cover the entire *projected* region of the alignment?

See Also

Other BString_functions: AAcoor2NAcoor_dFAST(), AAcoor2NAcoor_df(), AAcoor2NAcoor(), DF2XString(), XSDNARedunFilter(), XString2DF(), XString2KmerDT()

Examples

Trim2Core2

UriNeri/NeriMisc documentation built on Aug. 13, 2022, 4:37 p.m.