Updates Before Next iMSMS Batch #2
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Flags to disable time consuming steps Load new metadata rda file source mygsub define seqmeta$treatments define seqmeta$pms load map from Supplementary_datasets/map.txt Rebuild preprocessing so it can be run indepently on new dataset Define y as bray.list[[4]] in unifracPCA section Updated read xls to read_xlsx Restricted permanova to columns we care about Removed kegg label on bray.list[[1]] source diffPlot and abundancePlot Fix dots vs dashes in section 3.2.1 Update signFile and corresponding columns to a file generated by linear regression with current naming conventions Create output directories that don’t exist
…onni or FDR, ability to check bootstrap or wald confidence intervals
… new_batch_workflow/ code instead
… epsilon, enables checking code that's been ported over/modified
…OM models on specifically configured subsets of the data. Code to plot and compare the results. File declaring which gotus pass a 1 per 10000 abundance filter
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Updated libraries, cleaned up metagenomics workflow script to allow running up through linear regression calculations on a fresh install. Plotting code still doesn't work as yet from a clean R workspace and updated libraries.