In this repo, the data and code for producing the results of the manuscript Stability of the vaginal microbiota during pregnancy and its importance for early infant colonization by Mortensen et al (submitted to eLife - 2020).
The processed data is organized in a phyloseq object and can be downloaded from https://nc.copsac.com/index.php/s/foXTpYc65tBFq2k:
download.file('https://nc.copsac.com/index.php/s/foXTpYc65tBFq2k',paste(getwd(),'COPSACbirthmicrobiome_ASV.RData',sep = '/'))
load('COPSACbirthmicrobiome_ASV.RData')The code for running the analysis is found in the markdown document results_and_figures.md including costumized functions. Additionally, three files; getTransferStats.R, getWinnerStats.R and inferenceTransferStat.R are used for the analysis.
These are also build into an R-package MBtransfeR
devtools::install_github('mortenarendt/MBtransfeR')
library(MBtransfeR)The Raw sequence data is to be found on XX XX.
phy1 <- subset_samples(phyX, Type=='V' & Time == '36' & DELIVERY=='Normal')
phy2 <- subset_samples(phyX, Type=='F' & Time == '1w' & DELIVERY=='Normal')Here we use only a few permutations as this is time consuming. However, if you want to get proper inference set nperm to at least 1000.
res <- randpermutationTransferStats(phy1, phy2, 'dyadnb', nperm = 3)