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.
1 | OnePassProfiling(File = "HGB_0013_GXJPMPL01A3OQX.fasta", minseq = 21, entropymin = 0.6, Plot = TRUE)
|
File |
character. path to file. |
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. |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 | OnePass <- OnePassProfiling( #to be saved as a new function!!!
File="E:\Oligotyping\OT.180OTU_fasta\arbTrimmedFASTAsForOligotyping\HGB_0013_GXJPMPL01A3OQX.fasta",
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" ...
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