geneUsage: Gene usage.
In tcR: Advanced Data Analysis of Immune Receptor Repertoires
Description
Usage
Arguments
Value
See Also
Examples
Description
Compute frequencies or counts of gene segments ("V / J - usage").
Usage
1
2
3
4
5
6
7
geneUsage(
.data,
.genes = HUMAN_TRBV_MITCR,
.quant = c(NA, "read.count", "umi.count", "read.prop", "umi.prop"),
.norm = F,
.ambig = F
)
Arguments
.data
Cloneset data frame or a list with clonesets.
.genes
Either one of the gene alphabet (e.g., HUMAN_TRBV, genealphabets) or list with two gene alphabets for computing
joint distribution.
.quant
Which column to use for the quantity of clonotypes: NA for computing only number of genes without using clonotype counts,
"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.
.norm
If T then return proportions of resulting counting of genes.
.ambig
If F than remove from counting genes which are not presented in the given gene alphabet(s).
Value
If .data is a cloneset and .genes is NOT a list than return a data frame with first column "Gene" with genes and second with counts / proportions.
If .data is a list with clonesets and .genes is NOT a list than return a data frame with first column "Gene"
with genes and other columns with counts / proportions for each cloneset in the input list.
If .data is a cloneset and .genes IS a list than return a matrix with gene segments for the first gene in .genes
and column names for the second gene in .genes. See "Examples".
If .data is a list with clonesets and .genes IS a list than return a list with matrices like in the previous case.
See Also
genealphabets, vis.gene.usage, pca.segments
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
## Not run:
# Load your data
data(twb)
# compute V-segments frequencies of human TCR beta.
seg <- geneUsage(twb, HUMAN_TRBV, .norm = T)
# plot V-segments frequencies as a heatmap
vis.heatmap(seg, .labs = c("Sample", "V gene"))
# plot V-segments frequencies directly from clonesets
vis.gene.usage(twb, HUMAN_TRBV)
# plot V-segments frequencies from the gene frequencies
vis.gene.usage(seg, NA)
# Compute V-J joint usage.
geneUsage(twb, list(HUMAN_TRBV, HUMAN_TRBJ))
# for future:
# geneUsage(twb, "human", "trbv")
## 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: wc: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Could not detect number of cores, defaulting to 1.
Attaching package: 'tcR'
The following object is masked from 'package:igraph':
diversity
Warning: Ignoring unknown aesthetics: fill
Using Gene as id variables
Using Gene as id variables
$Subj.A
TRBJ1-1 TRBJ1-2 TRBJ1-3 TRBJ1-4 TRBJ1-5 TRBJ1-6 TRBJ2-1 TRBJ2-2
TRBV10-1 6 1 0 1 1 0 9 8
TRBV10-2 5 5 1 1 5 3 6 3
TRBV10-3 42 24 11 6 29 15 58 20
TRBV11-1 6 2 0 0 0 2 11 5
TRBV11-2 23 11 4 10 6 3 48 11
TRBV12-5 3 2 0 0 1 1 4 1
TRBV11-3 1 1 1 0 3 1 4 2
TRBV13 13 5 2 3 2 3 5 9
TRBV14 27 6 6 5 4 3 17 10
TRBV15 8 7 0 9 4 0 8 5
TRBV16 4 1 0 1 0 1 0 0
TRBV18 40 18 11 21 22 5 27 8
TRBV19 36 16 3 6 32 5 79 33
TRBV2 47 37 12 21 47 17 72 37
TRBV20-1 120 82 21 31 112 42 145 53
TRBV21-1 22 8 5 3 12 9 15 12
TRBV23-1 3 0 0 3 10 3 11 13
TRBV24-1 25 22 1 4 14 2 46 35
TRBV25-1 10 9 3 7 3 7 9 14
TRBV27 33 24 4 12 31 10 32 28
TRBV28 139 91 22 54 116 35 119 73
TRBV29-1 250 133 33 48 81 6 212 129
TRBV3-1 40 17 9 10 9 7 21 22
TRBV30 11 5 4 4 10 3 12 13
TRBV4-1 12 12 5 11 9 3 19 13
TRBV4-2 11 8 3 10 7 5 30 16
TRBV4-3 13 11 4 10 7 5 28 15
TRBV5-1 46 22 5 19 14 8 26 20
TRBV5-4 10 1 1 5 2 3 14 9
TRBV5-5 9 4 2 3 10 1 5 8
TRBV5-6 15 2 1 1 6 5 15 9
TRBV5-8 1 0 0 4 2 0 5 2
TRBV6-1 24 9 5 9 20 8 22 21
TRBV6-4 15 7 0 1 10 3 106 55
TRBV6-6 29 18 9 15 20 8 27 17
TRBV6-5 72 35 14 24 27 22 54 40
TRBV7-2 47 21 13 12 18 14 39 24
TRBV7-3 17 3 4 2 5 2 27 14
TRBV7-4 0 0 0 0 0 0 1 1
TRBV7-6 10 3 2 3 6 4 15 23
TRBV7-7 1 0 2 0 1 1 5 4
TRBV7-8 13 4 4 2 12 3 21 6
TRBV7-9 51 25 8 9 18 13 46 14
TRBV9 30 11 6 7 7 8 37 24
TRBV12-4 0 0 0 0 0 0 0 0
TRBV12-3 0 0 0 0 0 0 0 0
TRBV6-3 0 0 0 0 0 0 0 0
TRBV6-2 0 0 0 0 0 0 0 0
TRBV6-7 0 0 0 0 0 0 0 0
TRBJ2-3 TRBJ2-4 TRBJ2-5 TRBJ2-6 TRBJ2-7
TRBV10-1 9 0 1 0 4
TRBV10-2 7 0 6 0 6
TRBV10-3 29 0 16 3 55
TRBV11-1 6 1 3 0 7
TRBV11-2 20 5 18 0 27
TRBV12-5 2 0 0 0 1
TRBV11-3 2 0 3 0 2
TRBV13 7 2 9 0 8
TRBV14 12 4 5 0 14
TRBV15 12 0 5 1 3
TRBV16 0 0 0 0 1
TRBV18 30 2 13 0 24
TRBV19 28 6 7 2 33
TRBV2 61 12 23 2 43
TRBV20-1 99 20 51 8 166
TRBV21-1 15 5 11 1 23
TRBV23-1 7 4 4 0 7
TRBV24-1 32 2 14 0 14
TRBV25-1 8 0 2 1 10
TRBV27 22 2 17 3 38
TRBV28 82 16 52 9 185
TRBV29-1 170 21 79 5 146
TRBV3-1 23 2 7 2 15
TRBV30 16 0 2 2 14
TRBV4-1 10 2 4 0 21
TRBV4-2 25 1 6 5 21
TRBV4-3 17 5 6 7 24
TRBV5-1 29 1 11 2 27
TRBV5-4 12 1 3 0 6
TRBV5-5 11 0 0 1 2
TRBV5-6 4 0 2 1 12
TRBV5-8 2 3 0 0 3
TRBV6-1 22 1 8 5 19
TRBV6-4 121 1 3 4 8
TRBV6-6 13 4 9 3 16
TRBV6-5 38 2 14 2 48
TRBV7-2 42 9 17 3 42
TRBV7-3 23 2 7 1 3
TRBV7-4 0 0 0 0 0
TRBV7-6 11 0 7 0 17
TRBV7-7 3 0 4 0 1
TRBV7-8 7 1 6 0 21
TRBV7-9 36 4 15 1 29
TRBV9 24 2 11 4 22
TRBV12-4 0 0 0 0 0
TRBV12-3 0 0 0 0 0
TRBV6-3 0 0 0 0 0
TRBV6-2 0 0 0 0 0
TRBV6-7 0 0 0 0 0
$Subj.B
TRBJ1-1 TRBJ1-2 TRBJ1-3 TRBJ1-4 TRBJ1-5 TRBJ1-6 TRBJ2-1 TRBJ2-2
TRBV10-1 3 2 1 1 2 2 6 4
TRBV10-2 9 8 1 0 7 5 10 8
TRBV10-3 42 28 11 9 32 5 37 32
TRBV11-1 9 1 0 0 0 0 8 1
TRBV11-2 26 18 8 9 11 8 33 27
TRBV12-5 3 1 2 0 1 0 5 3
TRBV11-3 1 1 0 0 4 0 10 3
TRBV13 10 7 2 0 0 2 4 5
TRBV14 27 9 2 4 2 4 11 11
TRBV15 6 4 1 3 4 4 8 6
TRBV16 6 1 0 1 1 1 1 0
TRBV18 57 17 14 16 21 7 20 23
TRBV19 50 24 2 6 55 7 62 21
TRBV2 63 35 12 24 54 15 54 32
TRBV20-1 132 91 22 37 102 48 142 65
TRBV21-1 17 7 2 5 5 7 16 4
TRBV23-1 2 1 1 2 8 0 12 4
TRBV24-1 11 18 7 4 14 2 46 42
TRBV25-1 16 10 4 6 6 7 9 9
TRBV27 33 17 5 16 24 22 36 18
TRBV28 141 115 35 55 115 35 116 64
TRBV29-1 197 137 18 51 73 11 149 78
TRBV3-1 35 11 13 8 22 9 26 15
TRBV30 17 7 4 4 18 6 17 7
TRBV4-1 14 11 2 5 9 6 16 11
TRBV4-2 15 16 5 6 8 2 20 9
TRBV4-3 23 18 11 12 6 12 19 17
TRBV5-1 72 27 7 21 10 15 36 30
TRBV5-4 10 2 3 8 0 3 17 5
TRBV5-5 8 12 1 1 4 1 8 8
TRBV5-6 10 7 2 2 11 2 21 10
TRBV5-8 0 1 1 0 0 2 2 0
TRBV6-1 26 11 12 10 30 11 18 17
TRBV6-4 14 7 0 2 8 4 59 56
TRBV6-6 38 16 12 9 27 9 19 14
TRBV6-5 65 45 19 12 31 22 53 29
TRBV6-7 1 0 0 0 0 0 0 0
TRBV7-1 0 0 0 0 0 0 0 1
TRBV7-2 45 25 13 23 25 9 42 35
TRBV7-3 12 5 4 1 1 3 21 19
TRBV7-4 2 2 0 0 0 0 0 0
TRBV7-6 7 4 4 2 4 5 18 15
TRBV7-7 4 0 0 1 4 0 1 9
TRBV7-8 11 2 4 4 8 4 23 8
TRBV7-9 42 14 8 15 22 10 42 16
TRBV9 21 21 5 6 12 7 37 34
TRBV12-4 0 0 0 0 0 0 0 0
TRBV12-3 0 0 0 0 0 0 0 0
TRBV6-3 0 0 0 0 0 0 0 0
TRBJ2-3 TRBJ2-4 TRBJ2-5 TRBJ2-6 TRBJ2-7
TRBV10-1 7 0 1 0 6
TRBV10-2 8 1 1 0 7
TRBV10-3 35 2 18 3 53
TRBV11-1 4 1 4 0 6
TRBV11-2 38 7 17 1 27
TRBV12-5 2 0 1 0 4
TRBV11-3 2 0 1 0 1
TRBV13 2 0 1 0 6
TRBV14 10 4 6 1 16
TRBV15 9 1 5 1 6
TRBV16 1 0 0 1 2
TRBV18 24 2 14 1 23
TRBV19 24 2 7 2 32
TRBV2 51 3 21 0 40
TRBV20-1 122 25 39 7 133
TRBV21-1 17 5 7 1 15
TRBV23-1 8 0 7 0 10
TRBV24-1 28 1 7 0 13
TRBV25-1 9 2 4 0 12
TRBV27 30 3 14 2 35
TRBV28 84 19 47 13 169
TRBV29-1 132 20 71 12 111
TRBV3-1 29 7 12 1 18
TRBV30 8 1 5 4 12
TRBV4-1 13 5 8 0 21
TRBV4-2 41 0 9 5 13
TRBV4-3 21 0 11 8 16
TRBV5-1 41 4 11 2 39
TRBV5-4 16 1 7 1 9
TRBV5-5 11 0 2 1 10
TRBV5-6 7 1 7 1 17
TRBV5-8 1 7 2 0 1
TRBV6-1 19 1 12 1 22
TRBV6-4 95 4 1 8 6
TRBV6-6 24 3 9 1 23
TRBV6-5 44 4 27 10 57
TRBV6-7 0 0 0 0 0
TRBV7-1 0 0 0 0 0
TRBV7-2 65 5 27 2 43
TRBV7-3 30 1 3 4 9
TRBV7-4 1 0 0 0 1
TRBV7-6 9 0 10 0 15
TRBV7-7 4 0 1 0 1
TRBV7-8 13 2 3 0 13
TRBV7-9 42 7 9 0 19
TRBV9 37 2 10 0 21
TRBV12-4 0 0 0 0 0
TRBV12-3 0 0 0 0 0
TRBV6-3 0 0 0 0 0
$Subj.C
TRBJ1-1 TRBJ1-2 TRBJ1-3 TRBJ1-4 TRBJ1-5 TRBJ1-6 TRBJ2-1 TRBJ2-2
TRBV10-1 1 2 0 0 2 0 3 1
TRBV10-2 6 2 0 2 1 1 1 1
TRBV10-3 50 20 15 17 28 14 49 33
TRBV11-1 10 0 1 0 1 0 9 4
TRBV11-2 39 13 4 6 6 5 40 32
TRBV12-5 8 2 0 2 11 1 4 7
TRBV11-3 3 0 1 1 3 0 7 8
TRBV13 12 3 0 2 2 2 3 4
TRBV14 22 10 3 4 7 4 14 17
TRBV15 6 1 7 5 6 1 5 3
TRBV16 4 0 0 1 0 0 0 0
TRBV18 45 16 5 16 19 3 22 15
TRBV19 51 17 8 6 40 6 22 26
TRBV2 97 39 14 30 57 18 59 63
TRBV20-1 243 104 43 61 107 31 138 90
TRBV21-1 16 10 3 10 17 2 13 9
TRBV23-1 0 0 0 2 3 0 2 0
TRBV24-1 12 11 2 2 11 1 22 21
TRBV25-1 30 9 6 6 17 7 19 13
TRBV27 34 16 4 12 32 8 12 14
TRBV28 101 48 22 34 84 19 54 53
TRBV29-1 246 96 37 46 48 10 95 57
TRBV3-1 66 23 13 13 20 8 41 31
TRBV30 10 4 1 2 5 0 3 7
TRBV4-1 70 38 13 36 25 11 20 25
TRBV4-2 19 8 1 6 7 5 16 16
TRBV4-3 35 22 22 21 14 12 35 41
TRBV5-1 196 65 25 52 28 26 117 106
TRBV5-4 6 2 0 1 0 0 8 3
TRBV5-5 10 4 0 0 1 0 3 3
TRBV5-6 16 4 3 4 6 2 12 8
TRBV5-8 7 0 0 1 0 0 0 0
TRBV6-1 21 9 8 2 25 3 11 17
TRBV6-4 10 3 2 2 13 1 28 27
TRBV6-6 37 20 7 19 27 7 12 12
TRBV6-5 46 21 11 21 17 9 18 23
TRBV6-7 0 0 1 1 0 0 1 0
TRBV7-2 63 36 35 28 36 17 55 38
TRBV7-3 11 0 1 1 4 1 5 4
TRBV7-4 0 0 0 0 1 0 0 1
TRBV7-6 11 0 4 2 5 3 3 6
TRBV7-7 6 0 0 0 0 0 11 3
TRBV7-8 15 6 6 9 6 4 10 9
TRBV7-9 75 23 16 23 18 6 24 16
TRBV9 39 20 16 5 14 9 40 31
TRBV12-4 0 0 0 0 0 0 0 0
TRBV12-3 0 0 0 0 0 0 0 0
TRBV6-3 0 0 0 0 0 0 0 0
TRBV6-2 0 0 0 0 0 0 0 0
TRBJ2-3 TRBJ2-4 TRBJ2-5 TRBJ2-6 TRBJ2-7
TRBV10-1 0 0 0 0 0
TRBV10-2 3 0 3 1 1
TRBV10-3 48 3 15 0 36
TRBV11-1 5 0 0 1 2
TRBV11-2 31 7 14 1 25
TRBV12-5 2 0 0 0 0
TRBV11-3 2 1 1 0 0
TRBV13 7 0 2 0 7
TRBV14 10 0 3 0 14
TRBV15 7 1 1 0 3
TRBV16 1 1 0 0 2
TRBV18 22 4 8 1 19
TRBV19 17 1 8 2 13
TRBV2 53 9 21 0 35
TRBV20-1 151 15 83 2 117
TRBV21-1 8 2 8 0 17
TRBV23-1 0 0 0 0 2
TRBV24-1 23 3 4 1 2
TRBV25-1 24 3 10 1 29
TRBV27 21 4 3 0 16
TRBV28 71 12 29 4 63
TRBV29-1 134 11 65 6 58
TRBV3-1 30 4 17 1 31
TRBV30 2 1 2 0 0
TRBV4-1 47 3 9 1 29
TRBV4-2 17 2 5 2 15
TRBV4-3 38 2 9 2 15
TRBV5-1 162 8 16 4 69
TRBV5-4 4 0 1 0 0
TRBV5-5 5 1 1 0 1
TRBV5-6 8 1 0 1 7
TRBV5-8 2 0 0 0 0
TRBV6-1 10 1 2 2 3
TRBV6-4 31 0 0 2 2
TRBV6-6 27 4 8 0 11
TRBV6-5 27 2 3 1 13
TRBV6-7 0 0 0 0 0
TRBV7-2 98 13 9 0 29
TRBV7-3 8 1 0 2 1
TRBV7-4 0 0 0 0 0
TRBV7-6 3 0 2 0 7
TRBV7-7 3 0 1 0 3
TRBV7-8 14 2 2 0 4
TRBV7-9 28 3 7 0 16
TRBV9 42 0 7 0 14
TRBV12-4 0 0 0 0 0
TRBV12-3 0 0 0 0 0
TRBV6-3 0 0 0 0 0
TRBV6-2 0 0 0 0 0
$Subj.D
TRBJ1-1 TRBJ1-2 TRBJ1-3 TRBJ1-4 TRBJ1-5 TRBJ1-6 TRBJ2-1 TRBJ2-2
TRBV10-1 12 5 2 4 5 1 8 3
TRBV10-2 4 9 0 1 1 0 4 4
TRBV10-3 59 21 12 14 31 3 38 14
TRBV11-1 3 1 0 0 1 1 0 1
TRBV11-2 29 11 1 4 2 4 22 22
TRBV12-5 5 3 1 1 3 2 4 4
TRBV11-3 4 0 0 2 3 1 9 3
TRBV13 15 4 1 2 1 2 2 5
TRBV14 13 8 4 3 2 1 15 7
TRBV15 9 7 4 4 5 4 12 7
TRBV16 2 1 1 0 1 0 0 0
TRBV18 63 18 5 14 13 6 24 10
TRBV19 31 12 2 3 14 1 15 7
TRBV2 46 36 14 15 39 17 45 38
TRBV20-1 197 93 33 37 85 39 166 77
TRBV21-1 51 39 8 9 42 8 35 20
TRBV23-1 2 3 0 0 2 3 2 0
TRBV24-1 5 3 0 1 2 1 11 6
TRBV25-1 77 19 28 33 41 19 53 40
TRBV27 30 12 2 8 18 3 9 3
TRBV28 155 99 28 38 110 38 65 76
TRBV29-1 373 199 50 79 76 18 167 135
TRBV3-1 47 25 10 11 16 3 40 23
TRBV30 19 5 0 3 5 1 6 20
TRBV4-1 44 19 12 17 28 3 26 14
TRBV4-2 18 9 1 9 4 7 26 25
TRBV4-3 38 20 11 18 8 8 60 27
TRBV5-1 82 35 6 17 17 11 59 43
TRBV5-4 7 7 0 1 0 0 4 0
TRBV5-5 6 1 1 1 2 2 11 4
TRBV5-6 5 3 1 1 4 1 8 5
TRBV5-8 0 1 0 0 1 0 1 0
TRBV6-1 15 6 1 2 11 6 21 15
TRBV6-4 25 8 1 3 11 4 79 59
TRBV6-6 31 15 6 14 19 10 19 11
TRBV6-5 25 22 5 8 19 8 25 21
TRBV6-7 1 1 1 0 1 0 0 0
TRBV7-1 1 0 0 0 0 0 0 0
TRBV7-2 52 48 12 11 18 17 37 26
TRBV7-3 16 6 1 2 6 2 14 12
TRBV7-4 2 0 0 1 0 0 2 0
TRBV7-6 4 3 1 1 3 1 6 5
TRBV7-7 1 0 0 1 1 0 2 3
TRBV7-8 17 8 1 1 2 4 13 5
TRBV7-9 49 22 8 21 15 9 32 10
TRBV9 34 17 7 9 6 6 21 14
TRBV12-4 0 0 0 0 0 0 0 0
TRBV12-3 0 0 0 0 0 0 0 0
TRBV6-3 0 0 0 0 0 0 0 0
TRBJ2-3 TRBJ2-4 TRBJ2-5 TRBJ2-6 TRBJ2-7
TRBV10-1 1 2 0 1 5
TRBV10-2 3 0 2 0 5
TRBV10-3 31 2 16 3 30
TRBV11-1 0 0 1 0 0
TRBV11-2 27 0 5 3 21
TRBV12-5 4 0 1 1 2
TRBV11-3 8 0 2 0 5
TRBV13 10 1 2 0 5
TRBV14 14 0 9 0 10
TRBV15 16 2 2 1 10
TRBV16 0 0 0 1 2
TRBV18 23 3 11 2 24
TRBV19 9 1 2 0 7
TRBV2 49 5 29 1 41
TRBV20-1 117 9 68 3 109
TRBV21-1 24 7 12 2 37
TRBV23-1 1 1 2 1 4
TRBV24-1 5 1 1 2 1
TRBV25-1 54 11 19 3 50
TRBV27 12 4 4 0 13
TRBV28 90 7 33 7 99
TRBV29-1 249 20 67 12 82
TRBV3-1 27 4 11 1 26
TRBV30 7 0 2 4 6
TRBV4-1 34 1 11 2 9
TRBV4-2 36 4 10 5 18
TRBV4-3 38 2 9 9 41
TRBV5-1 84 11 8 1 37
TRBV5-4 6 0 0 0 3
TRBV5-5 6 0 2 1 5
TRBV5-6 6 1 1 0 1
TRBV5-8 0 0 0 0 2
TRBV6-1 15 0 2 3 8
TRBV6-4 100 2 5 4 7
TRBV6-6 18 1 3 1 23
TRBV6-5 15 3 12 6 22
TRBV6-7 1 0 0 0 1
TRBV7-1 0 0 0 0 0
TRBV7-2 97 12 23 4 49
TRBV7-3 15 2 8 2 6
TRBV7-4 1 0 1 0 0
TRBV7-6 4 0 2 0 7
TRBV7-7 1 0 5 1 3
TRBV7-8 14 1 2 1 6
TRBV7-9 20 4 7 2 32
TRBV9 21 3 10 2 11
TRBV12-4 0 0 0 0 0
TRBV12-3 0 0 0 0 0
TRBV6-3 0 0 0 0 0
tcR documentation built on July 2, 2020, 3:18 a.m.
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Description Usage Arguments Value See Also Examples
Description
Compute frequencies or counts of gene segments ("V / J - usage").
Usage
1 2 3 4 5 6 7 | geneUsage(
.data,
.genes = HUMAN_TRBV_MITCR,
.quant = c(NA, "read.count", "umi.count", "read.prop", "umi.prop"),
.norm = F,
.ambig = F
)
|
Arguments
.data |
Cloneset data frame or a list with clonesets. |
.genes |
Either one of the gene alphabet (e.g., HUMAN_TRBV, genealphabets) or list with two gene alphabets for computing joint distribution. |
.quant |
Which column to use for the quantity of clonotypes: NA for computing only number of genes without using clonotype counts, "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. |
.norm |
If T then return proportions of resulting counting of genes. |
.ambig |
If F than remove from counting genes which are not presented in the given gene alphabet(s). |
Value
If .data is a cloneset and .genes is NOT a list than return a data frame with first column "Gene" with genes and second with counts / proportions.
If .data is a list with clonesets and .genes is NOT a list than return a data frame with first column "Gene"
with genes and other columns with counts / proportions for each cloneset in the input list.
If .data is a cloneset and .genes IS a list than return a matrix with gene segments for the first gene in .genes
and column names for the second gene in .genes. See "Examples".
If .data is a list with clonesets and .genes IS a list than return a list with matrices like in the previous case.
See Also
genealphabets, vis.gene.usage, pca.segments
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## Not run:
# Load your data
data(twb)
# compute V-segments frequencies of human TCR beta.
seg <- geneUsage(twb, HUMAN_TRBV, .norm = T)
# plot V-segments frequencies as a heatmap
vis.heatmap(seg, .labs = c("Sample", "V gene"))
# plot V-segments frequencies directly from clonesets
vis.gene.usage(twb, HUMAN_TRBV)
# plot V-segments frequencies from the gene frequencies
vis.gene.usage(seg, NA)
# Compute V-J joint usage.
geneUsage(twb, list(HUMAN_TRBV, HUMAN_TRBJ))
# for future:
# geneUsage(twb, "human", "trbv")
## 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: wc: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Could not detect number of cores, defaulting to 1.
Attaching package: 'tcR'
The following object is masked from 'package:igraph':
diversity
Warning: Ignoring unknown aesthetics: fill
Using Gene as id variables
Using Gene as id variables
$Subj.A
TRBJ1-1 TRBJ1-2 TRBJ1-3 TRBJ1-4 TRBJ1-5 TRBJ1-6 TRBJ2-1 TRBJ2-2
TRBV10-1 6 1 0 1 1 0 9 8
TRBV10-2 5 5 1 1 5 3 6 3
TRBV10-3 42 24 11 6 29 15 58 20
TRBV11-1 6 2 0 0 0 2 11 5
TRBV11-2 23 11 4 10 6 3 48 11
TRBV12-5 3 2 0 0 1 1 4 1
TRBV11-3 1 1 1 0 3 1 4 2
TRBV13 13 5 2 3 2 3 5 9
TRBV14 27 6 6 5 4 3 17 10
TRBV15 8 7 0 9 4 0 8 5
TRBV16 4 1 0 1 0 1 0 0
TRBV18 40 18 11 21 22 5 27 8
TRBV19 36 16 3 6 32 5 79 33
TRBV2 47 37 12 21 47 17 72 37
TRBV20-1 120 82 21 31 112 42 145 53
TRBV21-1 22 8 5 3 12 9 15 12
TRBV23-1 3 0 0 3 10 3 11 13
TRBV24-1 25 22 1 4 14 2 46 35
TRBV25-1 10 9 3 7 3 7 9 14
TRBV27 33 24 4 12 31 10 32 28
TRBV28 139 91 22 54 116 35 119 73
TRBV29-1 250 133 33 48 81 6 212 129
TRBV3-1 40 17 9 10 9 7 21 22
TRBV30 11 5 4 4 10 3 12 13
TRBV4-1 12 12 5 11 9 3 19 13
TRBV4-2 11 8 3 10 7 5 30 16
TRBV4-3 13 11 4 10 7 5 28 15
TRBV5-1 46 22 5 19 14 8 26 20
TRBV5-4 10 1 1 5 2 3 14 9
TRBV5-5 9 4 2 3 10 1 5 8
TRBV5-6 15 2 1 1 6 5 15 9
TRBV5-8 1 0 0 4 2 0 5 2
TRBV6-1 24 9 5 9 20 8 22 21
TRBV6-4 15 7 0 1 10 3 106 55
TRBV6-6 29 18 9 15 20 8 27 17
TRBV6-5 72 35 14 24 27 22 54 40
TRBV7-2 47 21 13 12 18 14 39 24
TRBV7-3 17 3 4 2 5 2 27 14
TRBV7-4 0 0 0 0 0 0 1 1
TRBV7-6 10 3 2 3 6 4 15 23
TRBV7-7 1 0 2 0 1 1 5 4
TRBV7-8 13 4 4 2 12 3 21 6
TRBV7-9 51 25 8 9 18 13 46 14
TRBV9 30 11 6 7 7 8 37 24
TRBV12-4 0 0 0 0 0 0 0 0
TRBV12-3 0 0 0 0 0 0 0 0
TRBV6-3 0 0 0 0 0 0 0 0
TRBV6-2 0 0 0 0 0 0 0 0
TRBV6-7 0 0 0 0 0 0 0 0
TRBJ2-3 TRBJ2-4 TRBJ2-5 TRBJ2-6 TRBJ2-7
TRBV10-1 9 0 1 0 4
TRBV10-2 7 0 6 0 6
TRBV10-3 29 0 16 3 55
TRBV11-1 6 1 3 0 7
TRBV11-2 20 5 18 0 27
TRBV12-5 2 0 0 0 1
TRBV11-3 2 0 3 0 2
TRBV13 7 2 9 0 8
TRBV14 12 4 5 0 14
TRBV15 12 0 5 1 3
TRBV16 0 0 0 0 1
TRBV18 30 2 13 0 24
TRBV19 28 6 7 2 33
TRBV2 61 12 23 2 43
TRBV20-1 99 20 51 8 166
TRBV21-1 15 5 11 1 23
TRBV23-1 7 4 4 0 7
TRBV24-1 32 2 14 0 14
TRBV25-1 8 0 2 1 10
TRBV27 22 2 17 3 38
TRBV28 82 16 52 9 185
TRBV29-1 170 21 79 5 146
TRBV3-1 23 2 7 2 15
TRBV30 16 0 2 2 14
TRBV4-1 10 2 4 0 21
TRBV4-2 25 1 6 5 21
TRBV4-3 17 5 6 7 24
TRBV5-1 29 1 11 2 27
TRBV5-4 12 1 3 0 6
TRBV5-5 11 0 0 1 2
TRBV5-6 4 0 2 1 12
TRBV5-8 2 3 0 0 3
TRBV6-1 22 1 8 5 19
TRBV6-4 121 1 3 4 8
TRBV6-6 13 4 9 3 16
TRBV6-5 38 2 14 2 48
TRBV7-2 42 9 17 3 42
TRBV7-3 23 2 7 1 3
TRBV7-4 0 0 0 0 0
TRBV7-6 11 0 7 0 17
TRBV7-7 3 0 4 0 1
TRBV7-8 7 1 6 0 21
TRBV7-9 36 4 15 1 29
TRBV9 24 2 11 4 22
TRBV12-4 0 0 0 0 0
TRBV12-3 0 0 0 0 0
TRBV6-3 0 0 0 0 0
TRBV6-2 0 0 0 0 0
TRBV6-7 0 0 0 0 0
$Subj.B
TRBJ1-1 TRBJ1-2 TRBJ1-3 TRBJ1-4 TRBJ1-5 TRBJ1-6 TRBJ2-1 TRBJ2-2
TRBV10-1 3 2 1 1 2 2 6 4
TRBV10-2 9 8 1 0 7 5 10 8
TRBV10-3 42 28 11 9 32 5 37 32
TRBV11-1 9 1 0 0 0 0 8 1
TRBV11-2 26 18 8 9 11 8 33 27
TRBV12-5 3 1 2 0 1 0 5 3
TRBV11-3 1 1 0 0 4 0 10 3
TRBV13 10 7 2 0 0 2 4 5
TRBV14 27 9 2 4 2 4 11 11
TRBV15 6 4 1 3 4 4 8 6
TRBV16 6 1 0 1 1 1 1 0
TRBV18 57 17 14 16 21 7 20 23
TRBV19 50 24 2 6 55 7 62 21
TRBV2 63 35 12 24 54 15 54 32
TRBV20-1 132 91 22 37 102 48 142 65
TRBV21-1 17 7 2 5 5 7 16 4
TRBV23-1 2 1 1 2 8 0 12 4
TRBV24-1 11 18 7 4 14 2 46 42
TRBV25-1 16 10 4 6 6 7 9 9
TRBV27 33 17 5 16 24 22 36 18
TRBV28 141 115 35 55 115 35 116 64
TRBV29-1 197 137 18 51 73 11 149 78
TRBV3-1 35 11 13 8 22 9 26 15
TRBV30 17 7 4 4 18 6 17 7
TRBV4-1 14 11 2 5 9 6 16 11
TRBV4-2 15 16 5 6 8 2 20 9
TRBV4-3 23 18 11 12 6 12 19 17
TRBV5-1 72 27 7 21 10 15 36 30
TRBV5-4 10 2 3 8 0 3 17 5
TRBV5-5 8 12 1 1 4 1 8 8
TRBV5-6 10 7 2 2 11 2 21 10
TRBV5-8 0 1 1 0 0 2 2 0
TRBV6-1 26 11 12 10 30 11 18 17
TRBV6-4 14 7 0 2 8 4 59 56
TRBV6-6 38 16 12 9 27 9 19 14
TRBV6-5 65 45 19 12 31 22 53 29
TRBV6-7 1 0 0 0 0 0 0 0
TRBV7-1 0 0 0 0 0 0 0 1
TRBV7-2 45 25 13 23 25 9 42 35
TRBV7-3 12 5 4 1 1 3 21 19
TRBV7-4 2 2 0 0 0 0 0 0
TRBV7-6 7 4 4 2 4 5 18 15
TRBV7-7 4 0 0 1 4 0 1 9
TRBV7-8 11 2 4 4 8 4 23 8
TRBV7-9 42 14 8 15 22 10 42 16
TRBV9 21 21 5 6 12 7 37 34
TRBV12-4 0 0 0 0 0 0 0 0
TRBV12-3 0 0 0 0 0 0 0 0
TRBV6-3 0 0 0 0 0 0 0 0
TRBJ2-3 TRBJ2-4 TRBJ2-5 TRBJ2-6 TRBJ2-7
TRBV10-1 7 0 1 0 6
TRBV10-2 8 1 1 0 7
TRBV10-3 35 2 18 3 53
TRBV11-1 4 1 4 0 6
TRBV11-2 38 7 17 1 27
TRBV12-5 2 0 1 0 4
TRBV11-3 2 0 1 0 1
TRBV13 2 0 1 0 6
TRBV14 10 4 6 1 16
TRBV15 9 1 5 1 6
TRBV16 1 0 0 1 2
TRBV18 24 2 14 1 23
TRBV19 24 2 7 2 32
TRBV2 51 3 21 0 40
TRBV20-1 122 25 39 7 133
TRBV21-1 17 5 7 1 15
TRBV23-1 8 0 7 0 10
TRBV24-1 28 1 7 0 13
TRBV25-1 9 2 4 0 12
TRBV27 30 3 14 2 35
TRBV28 84 19 47 13 169
TRBV29-1 132 20 71 12 111
TRBV3-1 29 7 12 1 18
TRBV30 8 1 5 4 12
TRBV4-1 13 5 8 0 21
TRBV4-2 41 0 9 5 13
TRBV4-3 21 0 11 8 16
TRBV5-1 41 4 11 2 39
TRBV5-4 16 1 7 1 9
TRBV5-5 11 0 2 1 10
TRBV5-6 7 1 7 1 17
TRBV5-8 1 7 2 0 1
TRBV6-1 19 1 12 1 22
TRBV6-4 95 4 1 8 6
TRBV6-6 24 3 9 1 23
TRBV6-5 44 4 27 10 57
TRBV6-7 0 0 0 0 0
TRBV7-1 0 0 0 0 0
TRBV7-2 65 5 27 2 43
TRBV7-3 30 1 3 4 9
TRBV7-4 1 0 0 0 1
TRBV7-6 9 0 10 0 15
TRBV7-7 4 0 1 0 1
TRBV7-8 13 2 3 0 13
TRBV7-9 42 7 9 0 19
TRBV9 37 2 10 0 21
TRBV12-4 0 0 0 0 0
TRBV12-3 0 0 0 0 0
TRBV6-3 0 0 0 0 0
$Subj.C
TRBJ1-1 TRBJ1-2 TRBJ1-3 TRBJ1-4 TRBJ1-5 TRBJ1-6 TRBJ2-1 TRBJ2-2
TRBV10-1 1 2 0 0 2 0 3 1
TRBV10-2 6 2 0 2 1 1 1 1
TRBV10-3 50 20 15 17 28 14 49 33
TRBV11-1 10 0 1 0 1 0 9 4
TRBV11-2 39 13 4 6 6 5 40 32
TRBV12-5 8 2 0 2 11 1 4 7
TRBV11-3 3 0 1 1 3 0 7 8
TRBV13 12 3 0 2 2 2 3 4
TRBV14 22 10 3 4 7 4 14 17
TRBV15 6 1 7 5 6 1 5 3
TRBV16 4 0 0 1 0 0 0 0
TRBV18 45 16 5 16 19 3 22 15
TRBV19 51 17 8 6 40 6 22 26
TRBV2 97 39 14 30 57 18 59 63
TRBV20-1 243 104 43 61 107 31 138 90
TRBV21-1 16 10 3 10 17 2 13 9
TRBV23-1 0 0 0 2 3 0 2 0
TRBV24-1 12 11 2 2 11 1 22 21
TRBV25-1 30 9 6 6 17 7 19 13
TRBV27 34 16 4 12 32 8 12 14
TRBV28 101 48 22 34 84 19 54 53
TRBV29-1 246 96 37 46 48 10 95 57
TRBV3-1 66 23 13 13 20 8 41 31
TRBV30 10 4 1 2 5 0 3 7
TRBV4-1 70 38 13 36 25 11 20 25
TRBV4-2 19 8 1 6 7 5 16 16
TRBV4-3 35 22 22 21 14 12 35 41
TRBV5-1 196 65 25 52 28 26 117 106
TRBV5-4 6 2 0 1 0 0 8 3
TRBV5-5 10 4 0 0 1 0 3 3
TRBV5-6 16 4 3 4 6 2 12 8
TRBV5-8 7 0 0 1 0 0 0 0
TRBV6-1 21 9 8 2 25 3 11 17
TRBV6-4 10 3 2 2 13 1 28 27
TRBV6-6 37 20 7 19 27 7 12 12
TRBV6-5 46 21 11 21 17 9 18 23
TRBV6-7 0 0 1 1 0 0 1 0
TRBV7-2 63 36 35 28 36 17 55 38
TRBV7-3 11 0 1 1 4 1 5 4
TRBV7-4 0 0 0 0 1 0 0 1
TRBV7-6 11 0 4 2 5 3 3 6
TRBV7-7 6 0 0 0 0 0 11 3
TRBV7-8 15 6 6 9 6 4 10 9
TRBV7-9 75 23 16 23 18 6 24 16
TRBV9 39 20 16 5 14 9 40 31
TRBV12-4 0 0 0 0 0 0 0 0
TRBV12-3 0 0 0 0 0 0 0 0
TRBV6-3 0 0 0 0 0 0 0 0
TRBV6-2 0 0 0 0 0 0 0 0
TRBJ2-3 TRBJ2-4 TRBJ2-5 TRBJ2-6 TRBJ2-7
TRBV10-1 0 0 0 0 0
TRBV10-2 3 0 3 1 1
TRBV10-3 48 3 15 0 36
TRBV11-1 5 0 0 1 2
TRBV11-2 31 7 14 1 25
TRBV12-5 2 0 0 0 0
TRBV11-3 2 1 1 0 0
TRBV13 7 0 2 0 7
TRBV14 10 0 3 0 14
TRBV15 7 1 1 0 3
TRBV16 1 1 0 0 2
TRBV18 22 4 8 1 19
TRBV19 17 1 8 2 13
TRBV2 53 9 21 0 35
TRBV20-1 151 15 83 2 117
TRBV21-1 8 2 8 0 17
TRBV23-1 0 0 0 0 2
TRBV24-1 23 3 4 1 2
TRBV25-1 24 3 10 1 29
TRBV27 21 4 3 0 16
TRBV28 71 12 29 4 63
TRBV29-1 134 11 65 6 58
TRBV3-1 30 4 17 1 31
TRBV30 2 1 2 0 0
TRBV4-1 47 3 9 1 29
TRBV4-2 17 2 5 2 15
TRBV4-3 38 2 9 2 15
TRBV5-1 162 8 16 4 69
TRBV5-4 4 0 1 0 0
TRBV5-5 5 1 1 0 1
TRBV5-6 8 1 0 1 7
TRBV5-8 2 0 0 0 0
TRBV6-1 10 1 2 2 3
TRBV6-4 31 0 0 2 2
TRBV6-6 27 4 8 0 11
TRBV6-5 27 2 3 1 13
TRBV6-7 0 0 0 0 0
TRBV7-2 98 13 9 0 29
TRBV7-3 8 1 0 2 1
TRBV7-4 0 0 0 0 0
TRBV7-6 3 0 2 0 7
TRBV7-7 3 0 1 0 3
TRBV7-8 14 2 2 0 4
TRBV7-9 28 3 7 0 16
TRBV9 42 0 7 0 14
TRBV12-4 0 0 0 0 0
TRBV12-3 0 0 0 0 0
TRBV6-3 0 0 0 0 0
TRBV6-2 0 0 0 0 0
$Subj.D
TRBJ1-1 TRBJ1-2 TRBJ1-3 TRBJ1-4 TRBJ1-5 TRBJ1-6 TRBJ2-1 TRBJ2-2
TRBV10-1 12 5 2 4 5 1 8 3
TRBV10-2 4 9 0 1 1 0 4 4
TRBV10-3 59 21 12 14 31 3 38 14
TRBV11-1 3 1 0 0 1 1 0 1
TRBV11-2 29 11 1 4 2 4 22 22
TRBV12-5 5 3 1 1 3 2 4 4
TRBV11-3 4 0 0 2 3 1 9 3
TRBV13 15 4 1 2 1 2 2 5
TRBV14 13 8 4 3 2 1 15 7
TRBV15 9 7 4 4 5 4 12 7
TRBV16 2 1 1 0 1 0 0 0
TRBV18 63 18 5 14 13 6 24 10
TRBV19 31 12 2 3 14 1 15 7
TRBV2 46 36 14 15 39 17 45 38
TRBV20-1 197 93 33 37 85 39 166 77
TRBV21-1 51 39 8 9 42 8 35 20
TRBV23-1 2 3 0 0 2 3 2 0
TRBV24-1 5 3 0 1 2 1 11 6
TRBV25-1 77 19 28 33 41 19 53 40
TRBV27 30 12 2 8 18 3 9 3
TRBV28 155 99 28 38 110 38 65 76
TRBV29-1 373 199 50 79 76 18 167 135
TRBV3-1 47 25 10 11 16 3 40 23
TRBV30 19 5 0 3 5 1 6 20
TRBV4-1 44 19 12 17 28 3 26 14
TRBV4-2 18 9 1 9 4 7 26 25
TRBV4-3 38 20 11 18 8 8 60 27
TRBV5-1 82 35 6 17 17 11 59 43
TRBV5-4 7 7 0 1 0 0 4 0
TRBV5-5 6 1 1 1 2 2 11 4
TRBV5-6 5 3 1 1 4 1 8 5
TRBV5-8 0 1 0 0 1 0 1 0
TRBV6-1 15 6 1 2 11 6 21 15
TRBV6-4 25 8 1 3 11 4 79 59
TRBV6-6 31 15 6 14 19 10 19 11
TRBV6-5 25 22 5 8 19 8 25 21
TRBV6-7 1 1 1 0 1 0 0 0
TRBV7-1 1 0 0 0 0 0 0 0
TRBV7-2 52 48 12 11 18 17 37 26
TRBV7-3 16 6 1 2 6 2 14 12
TRBV7-4 2 0 0 1 0 0 2 0
TRBV7-6 4 3 1 1 3 1 6 5
TRBV7-7 1 0 0 1 1 0 2 3
TRBV7-8 17 8 1 1 2 4 13 5
TRBV7-9 49 22 8 21 15 9 32 10
TRBV9 34 17 7 9 6 6 21 14
TRBV12-4 0 0 0 0 0 0 0 0
TRBV12-3 0 0 0 0 0 0 0 0
TRBV6-3 0 0 0 0 0 0 0 0
TRBJ2-3 TRBJ2-4 TRBJ2-5 TRBJ2-6 TRBJ2-7
TRBV10-1 1 2 0 1 5
TRBV10-2 3 0 2 0 5
TRBV10-3 31 2 16 3 30
TRBV11-1 0 0 1 0 0
TRBV11-2 27 0 5 3 21
TRBV12-5 4 0 1 1 2
TRBV11-3 8 0 2 0 5
TRBV13 10 1 2 0 5
TRBV14 14 0 9 0 10
TRBV15 16 2 2 1 10
TRBV16 0 0 0 1 2
TRBV18 23 3 11 2 24
TRBV19 9 1 2 0 7
TRBV2 49 5 29 1 41
TRBV20-1 117 9 68 3 109
TRBV21-1 24 7 12 2 37
TRBV23-1 1 1 2 1 4
TRBV24-1 5 1 1 2 1
TRBV25-1 54 11 19 3 50
TRBV27 12 4 4 0 13
TRBV28 90 7 33 7 99
TRBV29-1 249 20 67 12 82
TRBV3-1 27 4 11 1 26
TRBV30 7 0 2 4 6
TRBV4-1 34 1 11 2 9
TRBV4-2 36 4 10 5 18
TRBV4-3 38 2 9 9 41
TRBV5-1 84 11 8 1 37
TRBV5-4 6 0 0 0 3
TRBV5-5 6 0 2 1 5
TRBV5-6 6 1 1 0 1
TRBV5-8 0 0 0 0 2
TRBV6-1 15 0 2 3 8
TRBV6-4 100 2 5 4 7
TRBV6-6 18 1 3 1 23
TRBV6-5 15 3 12 6 22
TRBV6-7 1 0 0 0 1
TRBV7-1 0 0 0 0 0
TRBV7-2 97 12 23 4 49
TRBV7-3 15 2 8 2 6
TRBV7-4 1 0 1 0 0
TRBV7-6 4 0 2 0 7
TRBV7-7 1 0 5 1 3
TRBV7-8 14 1 2 1 6
TRBV7-9 20 4 7 2 32
TRBV9 21 3 10 2 11
TRBV12-4 0 0 0 0 0
TRBV12-3 0 0 0 0 0
TRBV6-3 0 0 0 0 0
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