repOverlap: General function for the repertoire overlap evaluation.
In tcR: Advanced Data Analysis of Immune Receptor Repertoires
Description
Usage
Arguments
Details
See Also
Examples
Description
General interface to all cloneset overlap functions.
Usage
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repOverlap(
.data,
.method = c("exact", "hamm", "lev", "jaccard", "morisita", "tversky", "overlap",
"horn"),
.seq = c("nuc", "aa"),
.quant = c("read.count", "umi.count", "read.prop", "umi.prop"),
.vgene = F,
.norm = T,
.a = 0.5,
.b = 0.5,
.do.unique = T,
.verbose = T
)
Arguments
.data
List of clonesets.
.method
Which method to use for the overlap evaluation. See "Details" for methods.
.seq
Which clonotype sequences to use for the overlap: "nuc" for "CDR3.nucleotide.sequence", "aa" for
"CDR3.amino.acid.sequence".
.quant
Which column to use for the quantity of clonotypes: "read.count" for the "Read.count" column,
"umi.count" for the "Umi.count" column, "read.prop" for the "Read.proportion" column, "umi.prop" for
the "Umi.proportion" column. Used in "morisita" and "horn".
.vgene
If T than use V genes in computing shared or similar clonotypes. Used in all methods.
.norm
If T than compute the normalised number of shared clonotypes. Used in "exact".
.a, .b
Alpha and beta parameters for "tversky". Default values gives the Jaccard index measure.
.do.unique
If T than remove duplicates from the input data, but add their quantities to their clones.
.verbose
If T than output the data processing progress bar.
Details
You can see a more detailed description for each overlap method at intersectClonesets and similarity.
Parameter .method can have one of the following value each corresponding to the specific method:
- "exact" for the shared number of clonotypes (basic function intersectClonesets(..., .type = "..e")).
- "hamm" for the number of similar clonotypes by the Hamming distance (basic function intersectClonesets(..., .type = "..h")).
- "lev" for the number of similar clonotypes by the Levenshtein distance (basic function intersectClonesets(..., .type = "..l")).
- "jaccard" for the Jaccard index (basic function jaccard.index).
- "morisita" for the Morisita's overlap index (basic function morisita.index).
- "tversky" for the Tversky index (basic function tversky.index).
- "overlap" for the overlap coefficient (basic function overlap.coef).
- "horn" for the Horn's index (basic function horn.index).
See Also
intersectClonesets, similarity, repDiversity
Examples
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## Not run:
data(twb)
repOverlap(twb, "exact", .seq = "nuc", .vgene = F)
repOverlap(twb, "morisita", .seq = "aa", .vgene = T, .quant = "umi.count")
ov <- repOverlap(twb)
ov[is.na(ov)] <- 0
vis.pca(prcomp(ov, scale. = T), list(A = c(1, 2), B = c(3, 4)))
## End(Not run)
Example output
Loading required package: ggplot2
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: gridExtra
Attaching package: 'gridExtra'
The following object is masked from 'package:dplyr':
combine
Loading required package: reshape2
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:dplyr':
as_data_frame, groups, union
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
sh: 1: cannot create /dev/null: Permission denied
sh: 1: wc: Permission denied
Could not detect number of cores, defaulting to 1.
Attaching package: 'tcR'
The following object is masked from 'package:igraph':
diversity
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Subj.A Subj.B Subj.C Subj.D
Subj.A NA 4.6e-07 4.4e-07 4.0e-07
Subj.B 4.6e-07 NA 2.7e-07 2.7e-07
Subj.C 4.4e-07 2.7e-07 NA 6.2e-07
Subj.D 4.0e-07 2.7e-07 6.2e-07 NA
Preprocessing data...
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tcR documentation built on July 2, 2020, 3:18 a.m.
R Package Documentation
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Description Usage Arguments Details See Also Examples
Description
General interface to all cloneset overlap functions.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 | repOverlap(
.data,
.method = c("exact", "hamm", "lev", "jaccard", "morisita", "tversky", "overlap",
"horn"),
.seq = c("nuc", "aa"),
.quant = c("read.count", "umi.count", "read.prop", "umi.prop"),
.vgene = F,
.norm = T,
.a = 0.5,
.b = 0.5,
.do.unique = T,
.verbose = T
)
|
Arguments
.data |
List of clonesets. |
.method |
Which method to use for the overlap evaluation. See "Details" for methods. |
.seq |
Which clonotype sequences to use for the overlap: "nuc" for "CDR3.nucleotide.sequence", "aa" for "CDR3.amino.acid.sequence". |
.quant |
Which column to use for the quantity of clonotypes: "read.count" for the "Read.count" column, "umi.count" for the "Umi.count" column, "read.prop" for the "Read.proportion" column, "umi.prop" for the "Umi.proportion" column. Used in "morisita" and "horn". |
.vgene |
If T than use V genes in computing shared or similar clonotypes. Used in all methods. |
.norm |
If T than compute the normalised number of shared clonotypes. Used in "exact". |
.a, .b |
Alpha and beta parameters for "tversky". Default values gives the Jaccard index measure. |
.do.unique |
If T than remove duplicates from the input data, but add their quantities to their clones. |
.verbose |
If T than output the data processing progress bar. |
Details
You can see a more detailed description for each overlap method at intersectClonesets and similarity.
Parameter .method can have one of the following value each corresponding to the specific method:
- "exact" for the shared number of clonotypes (basic function intersectClonesets(..., .type = "..e")).
- "hamm" for the number of similar clonotypes by the Hamming distance (basic function intersectClonesets(..., .type = "..h")).
- "lev" for the number of similar clonotypes by the Levenshtein distance (basic function intersectClonesets(..., .type = "..l")).
- "jaccard" for the Jaccard index (basic function jaccard.index).
- "morisita" for the Morisita's overlap index (basic function morisita.index).
- "tversky" for the Tversky index (basic function tversky.index).
- "overlap" for the overlap coefficient (basic function overlap.coef).
- "horn" for the Horn's index (basic function horn.index).
See Also
intersectClonesets, similarity, repDiversity
Examples
1 2 3 4 5 6 7 8 9 | ## Not run:
data(twb)
repOverlap(twb, "exact", .seq = "nuc", .vgene = F)
repOverlap(twb, "morisita", .seq = "aa", .vgene = T, .quant = "umi.count")
ov <- repOverlap(twb)
ov[is.na(ov)] <- 0
vis.pca(prcomp(ov, scale. = T), list(A = c(1, 2), B = c(3, 4)))
## End(Not run)
|
Example output
Loading required package: ggplot2
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: gridExtra
Attaching package: 'gridExtra'
The following object is masked from 'package:dplyr':
combine
Loading required package: reshape2
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:dplyr':
as_data_frame, groups, union
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
sh: 1: cannot create /dev/null: Permission denied
sh: 1: wc: Permission denied
Could not detect number of cores, defaulting to 1.
Attaching package: 'tcR'
The following object is masked from 'package:igraph':
diversity
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Subj.A Subj.B Subj.C Subj.D
Subj.A NA 4.6e-07 4.4e-07 4.0e-07
Subj.B 4.6e-07 NA 2.7e-07 2.7e-07
Subj.C 4.4e-07 2.7e-07 NA 6.2e-07
Subj.D 4.0e-07 2.7e-07 6.2e-07 NA
Preprocessing data...
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Subj.A Subj.B Subj.C Subj.D
Subj.A NA NA NA NA
Subj.B NA NA NA NA
Subj.C NA NA NA NA
Subj.D NA NA NA NA
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R Package Documentation
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