OnePassProfilingMat: Provides oligotyping based on a one-pass entropy profiling,...
In aramette/otu2ot: Calculate oligotypes for aligned FASTA sequences

Description Usage Arguments Value Author(s) Examples

The function selects only the positions for which entropy is larger than a chosen cutoff. The positions are then aggregated to provide an oligotype identity. The function works on a alignment of sequences provided as a matrix object (see example).

1	OnePassProfilingMat(AlignedSequences = Sequences, minseq = 21, entropymin = 0.6, Plot = TRUE)

`AlignedSequences`	matrix. SequenceId-by-position matrix as produced by e.g. ImportFastaAlignmentImportFastaAlignment(). This is the main difference to MED(), the latter working on files and not on object in the current workspace.
`minseq`	numeric. minimum number of sequences before the procedure stops for a specific subalignment.
`entropymin`	numeric. minimum entropy level before the procedure stops for a specific subalignment.
`Plot`	logical. Plots the entropy profile, the base composition for the identified high entropy positions, and the histogram of relative abundance of concatenated oligotypes.:wq

A list with three slots:

`OT.seq.concat`	A vector of concatenated positions for each sequence.
`OT.count`	A summary table of overall abundance for each oligotype.
`OT.freq`	A summary table of overall frequency for each oligotype.

Alban Ramette

File="HGB_0013_GXJPMPL01A3OQX.fasta"
Aln.list<- ImportFastaAlignment(File) #path to FASTA file
Names <-  Aln.list[[1]]
Sequences <- toupper(Aln.list[[2]])# do not trim trailing dots at 5' and 3' ends
OnePass <- OnePassProfilingMat( 
  AlignedSequences=Sequences,
  minseq=21,
  entropymin=0.6,#arbitrary cutoff. the whole thing can be set in a function with a parameter specifying this cutoff.
  Plot=TRUE
)
#Position: 185 
#          A      G
#Nber 193.00 982.00
#Prop   0.17   0.87
#
#Position: 241 
#         A C G      U
#Nber 568.0 3 5 599.00
#Prop   0.5 0 0   0.53
#
#Position: 242 
#          - A C      G     U
#Nber 355.00 4 4 247.00 565.0
#Prop   0.31 0 0   0.22   0.5
#
#Position: 271 
#          - A      G
#Nber 818.00 2 355.00
#Prop   0.72 0   0.31
#
#Position: 272 
#          C G      U
#Nber 981.00 1 193.00
#Prop   0.87 0   0.17
#

str(OnePass)
#List of 3
# $ OT.seq.concat: Named chr [1:1175] "GAU-C" "GAU-C" "AUG-U" "AUG-U" ...
#  ..- attr(*, "names")= chr [1:1175] "1" "2" "3" "4" ...
# $ OT.count     : 'table' int [1:17(1d)] 1 1 1 1 1 188 4 562 1 2 ...
#  ..- attr(*, "dimnames")=List of 1
#  .. ..$ OT.seq.concat: chr [1:17] "AAU-C" "ACG-U" "AU--G" "AU-GC" ...
# $ OT.freq      : table [1:17(1d)] 0.000851 0.000851 0.000851 0.000851 0.000851 ...
#  ..- attr(*, "dimnames")=List of 1
#  .. ..$ OT.seq.concat: chr [1:17] "AAU-C" "ACG-U" "AU--G" "AU-GC" ...