I have a study with 150 files, meaning I need to process them in R. I saved the R code from a subset of 8 files on the GUI, but I haven’t been able to reproduce the results. I am trying to create a ASV/OTU table to proceed to microbial metabolomics
file_path<-“…/upload”
raw ← list.files(file_path, full.names = TRUE)
mbSet<-MicrobiomeAnalystR:::Init.mbSetObj()
mbSet<-MicrobiomeAnalystR:::SetModuleType(mbSet, “raw”)
MicrobiomeAnalystR:::ReadRawMeta(“metadata.txt”)
MicrobiomeAnalystR:::checkParing()
[1] 0
However, my data contains replicates, any advice on how to improve and/or fix my approach? A snipped of my metadata is below:
files parent_PFAS soil redox treatment/microbes week precursor concentration Pair
NAME_H1_1.fastq.gz FOSA Hudson N/A N/A 0 0 H1
NAME_H1_2.fastq.gz FOSA Hudson N/A N/A 0 0 H1