SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
Currently, L109-114 only make sense if you have 12 experimental and 12 control samples. It would make more sense to have a more general parsing such as:
divShannon_exp <- mean(diversity(flipped_complete_table[grep("exp",rownames(flipped_complete_table)),], index = "shannon"))
You just need to make sure your sample names contain "exp" and "control" in their names (note that I also had to modify the "GET FILE NAME" section, because currently it does not parse the information properly).
Finally, if you want this script to work with the Subsystems_results directory, you should modify Lines 66, 70,84,88 to add a "fill = T" argument (eg:
transcript
commented
6 years ago
Currently, L109-114 only make sense if you have 12 experimental and 12 control samples. It would make more sense to have a more general parsing such as: divShannon_exp <- mean(diversity(flipped_complete_table[grep("exp",rownames(flipped_complete_table)),], index = "shannon"))
You just need to make sure your sample names contain "exp" and "control" in their names (note that I also had to modify the "GET FILE NAME" section, because currently it does not parse the information properly).
Finally, if you want this script to work with the Subsystems_results directory, you should modify Lines 66, 70,84,88 to add a "fill = T" argument (eg:
control_table <- read.table(file = x, header = F, quote = "", sep = "\t",fill = T)
This would take care of rows that do not have a hierarchy ("NO HIERARCHY"). This is probably true in other scripts too.