odseq_unaligned: Outlier detection provided a distance/similarity matrix of...
In odseq: Outlier detection in multiple sequence alignments
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
View source: R/odseq_unaligned.R
Description
Provided a similarity matrix (like the ones provided using string kernels in kebabs). It will then compute a score for each sequence and perform bootstrap to provide information on the distribution of the scores, which is used to distinguish outlier sequences.
Usage
1
odseq_unaligned(distance_matrix, B = 100, threshold = 0.025, type = "similarity")
Arguments
distance_matrix
A numeric matrix representing either similarity or distance among unaligned sequences. Package kebabs may be useful for this task.
B
Integer indicating the number of bootstrap replicates to be run. The higher the more robust the detection should be.
threshold
Float indicating the probability to be left at the right of the bootstrap scores distribution when computing outliers. This parameter may need some tuning depending on each specific problem
type
A string indicating the type of distance metric used. Either 'similarity' or 'distance'.
Value
Returns a logical vector, where TRUE indicates an outlier.
Author(s)
Jos<c3><a9> Jim<c3><a9>nez <jose@jimenezluna.com>
References
[1] OD-seq: outlier detection in multiple sequence alignments. Peter Jehl, Fabian Sievers and Desmond G. Higgins. BMC Bioinformatics. 2015.
See Also
Examples
1
2
3
4
5
Example output
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: kernlab
Attaching package: 'kernlab'
The following object is masked from 'package:Biostrings':
type
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B0ZE05/1-76
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B1MUC0/1-76
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M7RET1/1-76
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M8QJN2/1-76
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Q9KJ82/1-76
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S4KUZ8/1-76
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Y1GKL8/1-76
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FALSE
A0A0A3ZSY6/1-77
FALSE
J5UN29/1-64
FALSE
C4K638/1-74
FALSE
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FALSE
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FALSE
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FALSE
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odseq documentation built on Nov. 8, 2020, 6:50 p.m.
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Description Usage Arguments Value Author(s) References See Also Examples
View source: R/odseq_unaligned.R
Description
Provided a similarity matrix (like the ones provided using string kernels in kebabs). It will then compute a score for each sequence and perform bootstrap to provide information on the distribution of the scores, which is used to distinguish outlier sequences.
Usage
1 | odseq_unaligned(distance_matrix, B = 100, threshold = 0.025, type = "similarity")
|
Arguments
distance_matrix |
A numeric matrix representing either similarity or distance among unaligned sequences. Package kebabs may be useful for this task. |
B |
Integer indicating the number of bootstrap replicates to be run. The higher the more robust the detection should be. |
threshold |
Float indicating the probability to be left at the right of the bootstrap scores distribution when computing outliers. This parameter may need some tuning depending on each specific problem |
type |
A string indicating the type of distance metric used. Either |
Value
Returns a logical vector, where TRUE indicates an outlier.
Author(s)
Jos<c3><a9> Jim<c3><a9>nez <jose@jimenezluna.com>
References
[1] OD-seq: outlier detection in multiple sequence alignments. Peter Jehl, Fabian Sievers and Desmond G. Higgins. BMC Bioinformatics. 2015.
See Also
Examples
1 2 3 4 5 |
Example output
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: kernlab
Attaching package: 'kernlab'
The following object is masked from 'package:Biostrings':
type
Q9F809/1-76
FALSE
D4I4P5/13-88
FALSE
E5BB17/42-117
FALSE
A0A0C8ZVD0/1-76
FALSE
A0A0F7JHC1/1-76
FALSE
B0ZE05/1-76
FALSE
B1MUC0/1-76
FALSE
M7RET1/1-76
FALSE
M8QJN2/1-76
FALSE
Q9KJ82/1-76
FALSE
S4KUZ8/1-76
FALSE
T2QBL4/1-76
FALSE
B0EYM2/1-76
FALSE
E9YM65/1-76
FALSE
A0A060RIR1/1-76
FALSE
A9LK87/1-76
FALSE
D8B5E1/1-76
FALSE
G3CAG9/1-76
FALSE
G3CAS3/1-76
FALSE
K3K332/1-76
FALSE
D0QML3/1-76
FALSE
G3CA69/1-76
FALSE
B4TLV4/1-76
FALSE
F0JY99/1-76
FALSE
E5YNK1/1-74
FALSE
Q70W75/1-74
FALSE
A0A0F5PHW8/1-74
FALSE
H3RLY1/1-76
FALSE
Y1GKL8/1-76
FALSE
A0A0E4G3K9/1-74
FALSE
A0A0A3ZSY6/1-77
FALSE
J5UN29/1-64
FALSE
C4K638/1-74
FALSE
A0A068Z196/1-75
FALSE
U2L622/1-77
FALSE
E6WMF1/1-77
FALSE
C9Y5R7/8-79
FALSE
A0A0F6VXC8/10-79
FALSE
R4IT59/8-78
FALSE
V5U7C5/1-63
FALSE
A0A0F8GEA6/1-78
FALSE
B2CBF1/1-79
FALSE
W8UA11/1-72
TRUE
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FALSE
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TRUE
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FALSE
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FALSE
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FALSE
D2TE61/2-68
FALSE
Q7X3U6/1-66
TRUE
Q8GEG7/1-66
TRUE
A0A085NVQ6/3-66
FALSE
D8ARD1/3-66
FALSE
E9TBD2/3-66
FALSE
I2WCR7/3-66
FALSE
T6L350/3-66
FALSE
T9A0E0/3-66
FALSE
H8NZG5/2-67
FALSE
H2J1I3/2-67
FALSE
A0A085G0L2/2-67
TRUE
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TRUE
A0A0D8ZNJ1/15-48
TRUE
K9ZRY5/6-50
TRUE
R6TXF2/28-77
TRUE
Q8YJV9/4-49
TRUE
A0A098J240/30-68
FALSE
F4Y0E3/13-51
TRUE
X6QB94/26-78
FALSE
K1ZNV2/51-98
TRUE
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TRUE
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TRUE
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TRUE
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TRUE
A0A060VI02/28-75
FALSE
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TRUE
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TRUE
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TRUE
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TRUE
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TRUE
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TRUE
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TRUE
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FALSE
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FALSE
U4M8Z1/28-66
FALSE
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FALSE
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TRUE
B7NZZ8/23-66
FALSE
H0FCF2/24-59
FALSE
T2AAN9/24-59
FALSE
G6FSM4/6-40
TRUE
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FALSE
A0A0F3Y7M4/31-66
FALSE
A1Y2U0/31-66
FALSE
H6BDZ3/31-66
FALSE
Q4W1Q5/31-66
FALSE
Q9XAW9/31-66
FALSE
A0A0D6YB80/6-40
TRUE
M5S0M0/30-72
TRUE
D7E264/9-49
TRUE
M0N320/2-44
TRUE
C8X5T5/33-69
FALSE
A0A0A3YL57/31-75
FALSE
X1VRR3/23-64
TRUE
A0A0F9QTI2/11-44
TRUE
A0A0C2QTU2/7-48
TRUE
A0A0C2R0C4/20-61
TRUE
A0A0D5A0A8/32-69
FALSE
A0A0F7KYP1/32-69
FALSE
B3GN64/21-66
FALSE
Q8GF42/21-66
FALSE
A0A0F8YVM5/8-42
TRUE
H1XN86/35-71
FALSE
A0A0A3WH88/35-82
FALSE
U4M7N6/35-82
FALSE
A0A0A1KP82/39-83
FALSE
C4K813/32-71
FALSE
Q8FLJ1/36-89
TRUE
X1EE99/7-45
TRUE
A0A073CA55/39-78
TRUE
V6AS99/13-47
TRUE
A3X2R3/39-78
FALSE
C8X5U4/15-69
TRUE
F7PJH7/2-44
TRUE
X0QTB5/19-68
FALSE
A0A0F8VDY7/10-45
TRUE
L7L2A9/46-83
TRUE
A0A061YVH7/27-66
FALSE
G4U4S9/27-66
FALSE
W4S9C4/27-66
FALSE
W4SGQ6/27-66
FALSE
V5XUV2/59-101
TRUE
K9YBZ8/616-662
TRUE
A0A0B3SGQ8/21-68
TRUE
Q0F3N8/3-47
TRUE
L7CIM3/27-75
FALSE
I1AZ85/17-67
TRUE
J2DK02/2-38
FALSE
U1Q8F3/2-43
TRUE
C6AEQ6/31-69
FALSE
K5D831/31-74
FALSE
A0A098I7P7/35-71
FALSE
A0A0B0J2G7/35-71
FALSE
M4U470/35-71
FALSE
K9YXZ0/584-635
TRUE
A0A0A2HZR0/2-45
TRUE
A0A0D6KFG1/24-57
TRUE
A0A0F4IEC9/21-64
TRUE
F9ZUV4/37-71
FALSE
K9W712/6-40
TRUE
E7PDY6/33-67
FALSE
Q88BQ0/33-67
FALSE
S6MVM0/33-67
FALSE
L7C888/21-67
TRUE
M3TUC6/43-86
TRUE
Q663B7/25-67
FALSE
A0A0F0GYE1/21-64
TRUE
A0A015X2U6/50-91
FALSE
A0A088F5T3/50-91
FALSE
B6W3D5/50-91
FALSE
C6IQM4/50-91
FALSE
C6Z9A5/50-91
FALSE
F3PNY5/50-91
FALSE
F7LMW8/50-91
FALSE
G6AV06/50-91
FALSE
G9S3I8/50-91
FALSE
I9AJH4/50-91
FALSE
K1FRK6/50-91
FALSE
S0FB78/50-91
FALSE
A0A096Y6L9/31-73
FALSE
A0A098KWW6/31-73
FALSE
A0A015UAT9/33-83
FALSE
A0A016CWP1/33-83
FALSE
B7AFD4/33-83
FALSE
E4VQV0/33-83
FALSE
I8YZQ4/33-83
FALSE
I9FBX3/33-83
FALSE
I9PU41/33-83
FALSE
K7X304/11-45
TRUE
A0A0D6YNY8/18-50
TRUE
A0A0D5NBM9/86-124
TRUE
Q74CF5/86-124
TRUE
A0A081BTE4/17-49
TRUE
A0A015ZBQ2/33-83
FALSE
B3JIP8/33-83
FALSE
D1K5Q2/33-83
FALSE
K1U5Q5/33-83
FALSE
A0A0C1QNN3/86-124
TRUE
Q6MCI6/5-39
TRUE
A0A0F4KHC3/23-64
TRUE
J0PP35/32-69
FALSE
A0A0F9GZY2/19-68
FALSE
X0R121/19-68
FALSE
A0A098J768/2-40
FALSE
B4V2V5/25-66
TRUE
J1IXM2/31-69
FALSE
J0Q1X0/32-68
FALSE
H9BQT8/15-66
TRUE
A0A0B2A0S2/29-74
FALSE
A0A0C1Q4C5/29-74
FALSE
B2UKE0/29-74
FALSE
C6BRA3/29-74
FALSE
R0CDV9/29-74
FALSE
S9RRB2/29-74
FALSE
U3G6E7/29-74
FALSE
R9WTK0/17-54
TRUE
A2C3W3/2-43
TRUE
random sequence 1 consisting of 100 residues.
TRUE
random sequence 2 consisting of 100 residues.
TRUE
random sequence 3 consisting of 100 residues.
TRUE
random sequence 4 consisting of 100 residues.
TRUE
random sequence 5 consisting of 100 residues.
TRUE
random sequence 6 consisting of 100 residues.
TRUE
random sequence 7 consisting of 100 residues.
TRUE
random sequence 8 consisting of 100 residues.
TRUE
random sequence 9 consisting of 100 residues.
TRUE
random sequence 10 consisting of 100 residues.
TRUE
random sequence 11 consisting of 100 residues.
TRUE
random sequence 12 consisting of 100 residues.
TRUE
random sequence 13 consisting of 100 residues.
TRUE
random sequence 14 consisting of 100 residues.
TRUE
random sequence 15 consisting of 100 residues.
TRUE
random sequence 16 consisting of 100 residues.
TRUE
random sequence 17 consisting of 100 residues.
TRUE
random sequence 18 consisting of 100 residues.
TRUE
random sequence 19 consisting of 100 residues.
TRUE
random sequence 20 consisting of 100 residues.
TRUE
random sequence 21 consisting of 100 residues.
TRUE
random sequence 22 consisting of 100 residues.
TRUE
random sequence 23 consisting of 100 residues.
TRUE
random sequence 24 consisting of 100 residues.
TRUE
random sequence 25 consisting of 100 residues.
TRUE
random sequence 26 consisting of 100 residues.
TRUE
random sequence 27 consisting of 100 residues.
TRUE
random sequence 28 consisting of 100 residues.
TRUE
random sequence 29 consisting of 100 residues.
TRUE
random sequence 30 consisting of 100 residues.
TRUE
random sequence 31 consisting of 100 residues.
TRUE
random sequence 32 consisting of 100 residues.
TRUE
random sequence 33 consisting of 100 residues.
TRUE
random sequence 34 consisting of 100 residues.
TRUE
random sequence 35 consisting of 100 residues.
TRUE
random sequence 36 consisting of 100 residues.
TRUE
random sequence 37 consisting of 100 residues.
TRUE
random sequence 38 consisting of 100 residues.
TRUE
random sequence 39 consisting of 100 residues.
TRUE
random sequence 40 consisting of 100 residues.
TRUE
random sequence 41 consisting of 100 residues.
TRUE
random sequence 42 consisting of 100 residues.
TRUE
random sequence 43 consisting of 100 residues.
TRUE
random sequence 44 consisting of 100 residues.
TRUE
random sequence 45 consisting of 100 residues.
TRUE
random sequence 46 consisting of 100 residues.
TRUE
random sequence 47 consisting of 100 residues.
TRUE
random sequence 48 consisting of 100 residues.
TRUE
random sequence 49 consisting of 100 residues.
TRUE
random sequence 50 consisting of 100 residues.
TRUE
random sequence 51 consisting of 100 residues.
TRUE
random sequence 52 consisting of 100 residues.
TRUE
random sequence 53 consisting of 100 residues.
TRUE
random sequence 54 consisting of 100 residues.
TRUE
random sequence 55 consisting of 100 residues.
TRUE
random sequence 56 consisting of 100 residues.
TRUE
random sequence 57 consisting of 100 residues.
TRUE
random sequence 58 consisting of 100 residues.
TRUE
random sequence 59 consisting of 100 residues.
TRUE
random sequence 60 consisting of 100 residues.
TRUE
random sequence 61 consisting of 100 residues.
TRUE
random sequence 62 consisting of 100 residues.
TRUE
random sequence 63 consisting of 100 residues.
TRUE
random sequence 64 consisting of 100 residues.
TRUE
random sequence 65 consisting of 100 residues.
TRUE
random sequence 66 consisting of 100 residues.
TRUE
random sequence 67 consisting of 100 residues.
TRUE
random sequence 68 consisting of 100 residues.
TRUE
random sequence 69 consisting of 100 residues.
TRUE
random sequence 70 consisting of 100 residues.
TRUE
random sequence 71 consisting of 100 residues.
TRUE
random sequence 72 consisting of 100 residues.
TRUE
random sequence 73 consisting of 100 residues.
TRUE
random sequence 74 consisting of 100 residues.
TRUE
random sequence 75 consisting of 100 residues.
TRUE
random sequence 76 consisting of 100 residues.
TRUE
random sequence 77 consisting of 100 residues.
TRUE
random sequence 78 consisting of 100 residues.
TRUE
random sequence 79 consisting of 100 residues.
TRUE
random sequence 80 consisting of 100 residues.
TRUE
random sequence 81 consisting of 100 residues.
TRUE
random sequence 82 consisting of 100 residues.
TRUE
random sequence 83 consisting of 100 residues.
TRUE
random sequence 84 consisting of 100 residues.
TRUE
random sequence 85 consisting of 100 residues.
TRUE
random sequence 86 consisting of 100 residues.
TRUE
random sequence 87 consisting of 100 residues.
TRUE
random sequence 88 consisting of 100 residues.
TRUE
random sequence 89 consisting of 100 residues.
TRUE
random sequence 90 consisting of 100 residues.
TRUE
random sequence 91 consisting of 100 residues.
TRUE
random sequence 92 consisting of 100 residues.
TRUE
random sequence 93 consisting of 100 residues.
TRUE
random sequence 94 consisting of 100 residues.
TRUE
random sequence 95 consisting of 100 residues.
TRUE
random sequence 96 consisting of 100 residues.
TRUE
random sequence 97 consisting of 100 residues.
TRUE
random sequence 98 consisting of 100 residues.
TRUE
random sequence 99 consisting of 100 residues.
TRUE
random sequence 100 consisting of 100 residues.
TRUE
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