SQMTOOLS selection

[Panda-smile]

library(SQMtools) sqm <- loadSQM("/mnt/hpc/home/zhanglj/squeezemetatrans/shotguntrans") sac = subsetTax(sqm, “class”, "Saccharomycetes") sac.carb = subsetFun(sac, "Carbohydrate metabolism")

First，Thanks to the professor careful guidance，my trouble as bellow：

To summarize the carbohydrate-related information including contig, orf, functional annotations (fun), and samples for all taxonomies at the species level under the class Saccharomyces into one table. How can I use combineSQM and export to do this? （I hope that the sorted data can be realized in the following table?）

[fpusan]

You don't need combineSQM for this. I think that running cbind over sac.carb$orfs$table, sac.carb$orfs$tax, and sac.carb$orfs$abund should give you something similar to what you describe. Take a look at all the tables within sac.carb$orfs. The structure of the SQM object and the information available within is described in the PDF manual for the SQMtools package, and in the wiki.

[fpusan]

Note also that species level classification will be probably unpractical (taxonomic annotation of individual contigs will usually not have enough resolution to grant a species-level classification) unless you really focus on bins.

[Panda-smile]

Thanks for the professor's suggestion, I'll try it now

[fpusan]

Closing due to lack of activity, feel free to reopen