Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
ClonalityDescriptionCreates a data frame giving the total number of sequences, number of unique productive sequences, number of genomes, entropy, clonality, Gini coefficient, and the frequency (%) of the top productive sequences in a list of sample data frames. Usageclonality(file.list) Arguments
DetailsClonality is derived from the Shannon entropy, which is calculated from the frequencies of all productive sequences divided by the logarithm of the total number of unique productive sequences. This normalized entropy value is then inverted (1 - normalized entropy) to produce the clonality metric. The Gini coefficient is an alternative metric used to calculate repertoire diversity and is derived from the Lorenz curve. The Lorenz curve is drawn such that x-axis represents the cumulative percentage of unique sequences and the y-axis represents the cumulative percentage of reads. A line passing through the origin with a slope of 1 reflects equal frequencies of all clones. The Gini coefficient is the ratio of the area between the line of equality and the observed Lorenz curve over the total area under the line of equality. Both Gini coefficient and clonality are reported on a scale from 0 to 1 where 0 indicates all sequences have the same frequency and 1 indicates the repertoire is dominated by a single sequence. ValueReturns a data frame giving the total number of sequences, number of unique productive sequences, number of genomes, entropy, clonality, Gini coefficient, and the frequency (%) of the top productive sequence in each sample. See Also
Examples
file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")
file.list <- readImmunoSeq(path = file.path)
clonality(file.list = file.list)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(LymphoSeq)
Loading required package: LymphoSeqDB
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LymphoSeq/clonality.Rd_%03d_medium.png", width=480, height=480)
> ### Name: clonality
> ### Title: Clonality
> ### Aliases: clonality
>
> ### ** Examples
>
> file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")
>
> file.list <- readImmunoSeq(path = file.path)
| | | 0% | |====== | 9% | |============= | 18% | |=================== | 27% | |========================= | 36% | |================================ | 45% | |====================================== | 55% | |============================================= | 64% | |=================================================== | 73% | |========================================================= | 82% | |================================================================ | 91% | |======================================================================| 100%
>
> clonality(file.list = file.list)
samples totalSequences uniqueProductiveSequences totalGenomes
1 TCRB_Day949_CD4 999 845 25767
2 TCRB_Day949_CD8 999 796 26236
3 TCRB_Day0_Unsorted 999 837 18215
4 TCRB_Day83_CD8_CMV 201 122 254
5 TCRB_Day32_Unsorted 920 767 NA
6 TCRB_Day369_CD8_CMV 414 281 1794
7 TCRB_Day83_Unsorted 999 830 NA
8 TCRB_Day1320_CD8_CMV 40 25 53
9 TCRB_Day369_Unsorted 999 828 NA
10 TCRB_Day949_Unsorted 999 831 6547
11 TCRB_Day1320_Unsorted 999 833 180079
totalCount entropy clonality giniCoefficient topProductiveSequence
1 1795561 5.597259 0.42431656 0.8486265 29.232143
2 2161314 5.535828 0.42554289 0.9018374 19.131268
3 1158510 7.144318 0.26416150 0.7956718 5.543769
4 4553 5.891883 0.14989093 0.6133629 8.917656
5 31078 8.296630 0.13424209 0.6007820 4.865016
6 52480 5.011083 0.38396606 0.8677666 17.718550
7 427427 7.285945 0.24863671 0.7100983 13.821673
8 53 4.486348 0.03391748 0.2313514 10.810811
9 725668 6.037979 0.37710971 0.8043414 17.568430
10 1486480 6.774799 0.30147383 0.7739322 13.510800
11 180079 5.708193 0.41165830 0.8845652 14.422142
>
>
>
>
>
> dev.off()
null device
1
>
|