sqm2tables.py, sqmreads2tables.py or combine-sqm-tables.py into R.This function takes the path to the output directory generated by sqm2tables.py, sqmreads2tables.py or combine-sqm-tables.py a SQMlite object.
The SQMlite object will contain taxonomic and functional profiles, but no detailed information on ORFs, contigs or bins. However, it will also have a much smaller memory footprint.
A SQMlite object can be used for plotting and exporting, but it can not be subsetted.
loadSQMlite(tables_path, tax_mode = "allfilter")SQMlite object containing the parsed tables.
character, tables directory generated by sqm2table.py, sqmreads2tables.py or combine-sqm-tables.py.
character, which taxonomic classification should be loaded? SqueezeMeta applies the identity thresholds described in Luo et al., 2014. Use allfilter for applying the minimum identity threshold to all taxa (default), prokfilter for applying the threshold to Bacteria and Archaea, but not to Eukaryotes, and nofilter for applying no thresholds at all.
The SQMlite object is a nested list which contains the following information:
| lvl1 | lvl2 | lvl3 | type | rows/names | columns | data |
| $taxa | $superkingdom | $abund | numeric matrix | superkingdoms | samples | abundances |
| $percent | numeric matrix | superkingdoms | samples | percentages | ||
| $phylum | $abund | numeric matrix | phyla | samples | abundances | |
| $percent | numeric matrix | phyla | samples | percentages | ||
| $class | $abund | numeric matrix | classes | samples | abundances | |
| $percent | numeric matrix | classes | samples | percentages | ||
| $order | $abund | numeric matrix | orders | samples | abundances | |
| $percent | numeric matrix | orders | samples | percentages | ||
| $family | $abund | numeric matrix | families | samples | abundances | |
| $percent | numeric matrix | families | samples | percentages | ||
| $genus | $abund | numeric matrix | genera | samples | abundances | |
| $percent | numeric matrix | genera | samples | percentages | ||
| $species | $abund | numeric matrix | species | samples | abundances | |
| $percent | numeric matrix | species | samples | percentages | ||
| $functions | $KEGG | $abund | numeric matrix | KEGG ids | samples | abundances (reads) |
| $bases | numeric matrix | KEGG ids | samples | abundances (bases) | ||
| $tpm | numeric matrix | KEGG ids | samples | tpm | ||
| $copy_number | numeric matrix | KEGG ids | samples | avg. copies | ||
| $COG | $abund | numeric matrix | COG ids | samples | abundances (reads) | |
| $bases | numeric matrix | COG ids | samples | abundances (bases) | ||
| $tpm | numeric matrix | COG ids | samples | tpm | ||
| $copy_number | numeric matrix | COG ids | samples | avg. copies | ||
| $PFAM | $abund | numeric matrix | PFAM ids | samples | abundances (reads) | |
| $bases | numeric matrix | PFAM ids | samples | abundances (bases) | ||
| $tpm | numeric matrix | PFAM ids | samples | tpm | ||
| $copy_number | numeric matrix | PFAM ids | samples | avg. copies | ||
| $total_reads | numeric vector | samples | (n/a) | total reads | ||
| $misc | $project_name | character vector | (empty) | (n/a) | project name | |
| $samples | character vector | (empty) | (n/a) | samples | ||
| $tax_names_long | $superkingdom | character vector | short names | (n/a) | full names | |
| $phylum | character vector | short names | (n/a) | full names | ||
| $class | character vector | short names | (n/a) | full names | ||
| $order | character vector | short names | (n/a) | full names | ||
| $family | character vector | short names | (n/a) | full names | ||
| $genus | character vector | short names | (n/a) | full names | ||
| $species | character vector | short names | (n/a) | full names | ||
| $tax_names_short | character vector | full names | (n/a) | short names | ||
| $KEGG_names | character vector | KEGG ids | (n/a) | KEGG names | ||
| $KEGG_paths | character vector | KEGG ids | (n/a) | KEGG hiararchy | ||
| $COG_names | character vector | COG ids | (n/a) | COG names | ||
| $COG_paths | character vector | COG ids | (n/a) | COG hierarchy | ||
| $ext_annot_sources | character vector | (empty) | (n/a) | external databases |
-extdb argument, the corresponding abundance, tpm and copy number profiles will be present in SQM$functions (e.g. results for the CAZy database would be present in SQM$functions$CAZy). Additionally, the extended names of the features present in the external database will be present in SQM$misc (e.g. SQM$misc$CAZy_names). Note that results generated by SqueezeMeta_reads will contain only read abundances, but not bases, tpm or copy number estimations.plotBars and plotFunctions will plot the most abundant taxa and functions in a SQMlite object. exportKrona will generate Krona charts reporting the taxonomy in a SQMlite object.