Dataset Open Access

SLAFEEL: R scripts and reformatted data analyzed by Alamil et al. (2019)

Maryam Alamil; Joseph Hughes; Karine Berthier; Cécile Desbiez; Gaël Thébaud; Samuel Soubeyrand

SLAFEEL: Statistical Learning Approach For Estimating Epidemiological Links from deep sequencing data

This archive contains R scripts for running analyses proposed by Alamil et al. (2019; Inferring epidemiological links from deep sequencing data: a statistical learning approach for human, animal and plant diseases), namely
- functions.R that contains R functions required for computations,
- influenza.R, ebola.R and potyvirus.R where the analyses are implemented for each case study, and
- influenza-format-genomic-data.R giving an example of how to format data to be used in the statistical learning approach.

This archive also contains the reformatted data analyzed by Alamil et al. (2019). The datasets that are provided concern swine influenza virus (reformatted from Murcia et al., 2012), Ebola virus (reformatted from Gire et al., 2014) and a wild salsify potyvirus. Two rds files are provided for swine influenza, the first one for the naive chain, the second one for the vaccinated chain. Ebola rds files are compressed into the archive ebolaRDS.zip. rds files can be loaded in the R statistical software with the command "readRDS(filename)", which returns a list. The list contains a "readme" item describing the contents of the list, as well as a "host.table" item providing metadata about host units and a "set.of.sequences" item providing sequencing data formatted in numeric matrices.

Murcia PR, Hughes J, Battista P, Lloyd L, Baillie GJ, Ramirez-Gonzalez RH, et al. Evolution of an Eurasian avian-like influenza virus in naive and vaccinated pigs. PLoS Pathogens. 2012;8(5):e1002730.

Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science. 2014;345:1369–1372

 

Funded by the ANR - Project name: SMITID (2016-2020) - Grant number: ANR-16-CE35-0006

Files (530.8 kB)
Name Size
ebola.R
md5:5c40bbb85b97e80d6fd2fa3472a6c3e5
2.4 kB Download
ebolaRDS.zip
md5:8616cde27972265bf8488787db679bf8
379.0 kB Download
functions.R
md5:8c8362d660fa13f05aba7050a2bb20e3
10.4 kB Download
influenza-format-genomic-data.R
md5:5ae6cc4786839dbc19b9b5da9d1e98dc
3.8 kB Download
influenza-raw-genomic-data.zip
md5:32e5e17c3d17f81374da97a561c723c1
34.4 kB Download
influenza.R
md5:9ffc47978cc8f080bf1e03194d675330
2.1 kB Download
potyvirus.R
md5:81bd3893a47cc1d05d21227a1b8db948
1.7 kB Download
potyvirus.rds
md5:c3e4fdce1b01e04b64c1cafd61c282f0
19.7 kB Download
swine-influenza_naive-chain.rds
md5:d7a249867208bc2bb150526b44d98053
27.8 kB Download
swine-influenza_vaccinated-chain.rds
md5:59219b8b46523b36551002bbc05b52c6
49.4 kB Download
  • Alamil M, Hughes J., Berthier K, Desbiez C, Thébaud G Soubeyrand S (2018) Inferring epidemiological links from deep sequencing data: a statistical learning approach for human, animal and plant diseases. Technical Report, BioSP, INRA, Avignon.

  • Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science. 2014;345:1369–1372

  • Murcia PR, Hughes J, Battista P, Lloyd L, Baillie GJ, Ramirez-Gonzalez RH, et al. Evolution of an Eurasian avian-like influenza virus in naive and vaccinated pigs. PLoS Pathogens. 2012;8(5):e1002730.

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