read.mothur.shared <- function(shared.file){ otu_data <-read.table(shared.file, header=T) %>% t(.) %>% .[2:nrow(.),] %>% .[-c(2),] %>% data.frame(.) colnames(otu_data) <- as.character(unlist(otu_data[1,])) otu_data <- otu_data[-1, ] write.csv(otu_data, file="otu_data.csv") otu_data <-read.csv("otu_data.csv", header=T, row.names = 1) otu_data <- data.frame(t(otu_data)) return(otu_data) }
library(devtools) install_github("ravinpoudel/myFunctions") library(myFunctions) library(igraph) library(magrittr) library(tidyverse) library(data.table)
# import count data with NOT using read.mothur.shared function otu_data.reg <- read.table(Sys.glob("*.shared"), sep = "\t") otu_data.reg[1:4, 1:3] # import count data with read.mothur.shared function otu_data.fn <- read.mothur.shared(Sys.glob("*.shared")) otu_data.fn[1:4, 1:3] # upload taxanomy file without using read.mothur.taxonomy function tax.reg <- read.delim(Sys.glob("*.taxonomy"), sep="\t", header=F) head(tax.reg) # upload taxanomy file using read.mothur.taxonomy function tax.fn <- read.mothur.taxonomy(Sys.glob("*.taxonomy")) head(tax.fn) # if everything went smoothly then rownames of these two files should get you a true output all.equal(colnames(otu_data.fn), rownames(tax.fn))
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