An R-script is covering the different steps of personal identification using human skin microbiome that as described in the article 'Environmental bacteria contribute personal identification of human skin microbiome'
We checked this Rscript can work on R version 3.3.2 and Rstdio version 1.1.338
The function of "personal_identification" require two kind of argument.
"d.dist.m.query_reference" is the matrix of canberra distance. The row is the query samples and column is reference samples. If there is the query sample in the reference samples, this function automatically remove the sample from reference sample when a query sample is calcurated mean of distance with reference each individual's one (reave-of-out).
A1 A2 ... C2 C3
A1 0 100 ... 200 230
A2 100 0 ... 220 230
: : : : :
C2 200 220 ... 0 90
C3 230 230 ... 90 0
"sample_individual" is relational table of samples and individuals.
sample individual
A1 A
A2 A
A3 A
B1 B
B2 B
B3 B
C1 C
C2 C
C3 C
This function returns two kinds of results as a list class. The $matrix shows how many samples of each individual are classified for each individual. The rows of this matrix are the number of query samples and the columns are the number of reference samples.
$matrix
A B C
A 1 0 0
B 0 1 0
C 0 0 1
The $score show accuracy of personal identification which is TP / (TP + FN)
$score
[1] 1
git clone https://github.com/yamada-lab/human_skin_personal_identification.git
If you want to show demonstration of our Rscript, please install Rstudio and perform our R Script (line 1 to 70).
created by Hikaru Watanabe at Tokyo Institute of Technology
BSD 3-Clause License
Copyright (c) 2017, HikaruWatanabe All rights reserved.
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