Commit 06ee0652 authored by Etienne Rifa's avatar Etienne Rifa
Browse files

resolve decontam + citation

multiple taxa manual filtering
issue raised by Olivier Navaud, thx!
parent 926a669c
Pipeline #35408 passed with stage
in 11 seconds
......@@ -294,14 +294,11 @@ decontam_fun <- function(data = data, domain = "Bacteria", output = "./decontam_
cont_list <- unlist(strsplit(manual_cont,","))
flog.info(paste('Removing ',cont_list, sep=''))
ttable = data@tax_table@.Data
taxToKeep5=NULL
for(i in cont_list){
if(manual_cont_rank == "ASV"){
taxToKeep5 = c(taxToKeep5,row.names(ttable)[row.names(ttable) !=i ] )
taxToKeep5 = !row.names(ttable) %in% cont_list
}else{
taxToKeep5 = c(taxToKeep5,row.names(ttable)[ttable[,manual_cont_rank]!=i])
taxToKeep5 = !ttable[,manual_cont_rank] %in% cont_list
}
}
data <- prune_taxa(taxToKeep5, data)
}
......
citHeader("To cite ranomaly in publications use:")
citEntry(
entry = "Article",
title = "RANOMALY: AmplicoN WOrkflow for Microbial Community AnaLYsis",
author = "Theil Sebastien and Rifa Etienne",
journal = "F1000Research",
year = "2021",
volume = "10",
page = "7",
url = "https://doi.org/10.12688/f1000research.27268.1",
textVersion = paste(
"Theil Sebastien, and Rifa Etienne. 2021. « RANOMALY: AmplicoN WOrkflow for Microbial Community AnaLYsis ». F1000Research 10 (january): 7. https://doi.org/10.12688/f1000research.27268.1."
)
)
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