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

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<br> - functions.R that contains R functions required for computations,<br> - influenza.R, ebola.R and potyvirus.R where the analyses are implemented for each case study, and<br> - 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-CE35-0006SLAFEEL：基于深度测序数据估算流行病学关联的统计学习方法 本归档文件包含用于复现Alamil等人2019年提出的分析方法的R脚本，相关研究论文为《基于深度测序数据推断流行病学关联：面向人畜及植物病害的统计学习方案》，具体包括： - functions.R：包含分析所需的R计算函数； - influenza.R、ebola.R与potyvirus.R：分别针对三个案例研究实现完整分析流程； - influenza-format-genomic-data.R：提供如何将测序数据格式化为适配该统计学习方法的示例脚本。 本归档文件同时包含Alamil等人2019年研究中使用的格式化后数据集。本次提供的数据集涵盖：猪流感病毒（数据源自Murcia等人2012年的研究，已完成格式重构）、埃博拉病毒（数据源自Gire等人2014年的研究，已完成格式重构）以及一种野生婆罗门参马铃薯Y病毒。 针对猪流感病毒，本次提供两个rds格式文件：前者对应未免疫宿主链，后者对应免疫宿主链。埃博拉病毒相关的rds格式文件已打包至ebolaRDS.zip归档文件中。rds格式文件可通过R统计软件的"readRDS(filename)"命令加载，加载后将返回一个列表对象。该列表包含一个"readme"条目用于描述列表内容，以及"host.table"条目提供宿主样本的元数据，还有"set.of.sequences"条目提供以数值矩阵形式格式化的测序数据。 Murcia PR, Hughes J, Battista P, Lloyd L, Baillie GJ, Ramirez-Gonzalez RH, 等. 欧亚禽源性流感病毒在未免疫与免疫猪体内的演化. PLoS Pathogens. 2012;8(5):e1002730. Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, 等. 基因组监测阐明2014年埃博拉病毒暴发期间的病毒起源与传播链. Science. 2014;345:1369–1372 本项目由法国国家研究署（ANR）资助，项目名称：SMITID（2016-2020），资助编号：ANR-16-CE35-0006