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Personal identification using human skin microbiome

overview

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'

Requirement

We checked this Rscript can work on R version 3.3.2 and Rstdio version 1.1.338

Usage

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

Installation

git clone https://github.com/yamada-lab/human_skin_personal_identification.git

DEMO

If you want to show demonstration of our Rscript, please install Rstudio and perform our R Script (line 1 to 70).

Author

created by Hikaru Watanabe at Tokyo Institute of Technology

License

BSD 3-Clause License

Copyright (c) 2017, HikaruWatanabe All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

  • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

  • Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.