# Analyze Results Generated by the 'SqueezeMeta' Pipeline

## Documentation for package ‘SQMtools’ version 1.8.0

- DESCRIPTION file.

## Help Pages

CheckMProkaryote | CheckM reference markers for Prokaryotes
combineSQM | Combine several SQM objects
combineSQMlite | Combine several SQM or SQMlite objects
create_bin | Create a bin from a vector of contigs
exportBins | Export the bins of a SQM object
exportContigs | Export the contigs of a SQM object
exportKrona | Export the taxonomy of a SQM object into a Krona Chart
exportORFs | Export the ORFs of a SQM object
exportPathway | Export the functions of a SQM object into KEGG pathway maps
exportTable | Export results in tabular format
find_redundant_contigs | Find redundant contigs within a bin
Hadza | Hadza hunter-gatherer gut metagenomes
loadSQM | Load a SqueezeMeta project into R
loadSQMlite | Load tables generated by 'sqm2tables.py', 'sqmreads2tables.py' or 'combine-sqm-tables.py' into R.
MGKOs | Single Copy Phylogenetic Marker Genes from Sunagawa's group (KOs)
MGOGs | Single Copy Phylogenetic Marker Genes from Sunagawa's group (OGs)
mostAbundant | Get the N most abundant rows (or columns) from a numeric table
mostVariable | Get the N most variable rows (or columns) from a numeric table
plotBars | Plot a barplot using ggplot2
plotBins | Barplot of the most abundant bins in a SQM object
plotFunctions | Heatmap of the most abundant functions in a SQM object
plotHeatmap | Plot a heatmap using ggplot2
plotTaxonomy | Barplot of the most abundant taxa in a SQM object
RecA | RecA/RadA recombinase
remove_contigs_from_bin | Remove contigs from a given bin
renameSamples | Change sample names
rowMaxs | Return a vector with the row-wise maxima of a matrix or dataframe.
rowMins | Return a vector with the row-wise minima of a matrix or dataframe.
seqvec2fasta | Print a named vector of sequences as a fasta-formatted string
SQM_to_microeco | Convert a SQM object into a microtable object from the _microeco_ package
SQM_to_phyloseq | Convert a SQM object into a phyloseq object from the _phyloseq_ package
subsetBins | Create a SQM object containing only the requested bins, and the contigs and ORFs contained in them.
subsetContigs | Select contigs
subsetFun | Filter results by function
subsetORFs | Select ORFs
subsetRand | Select random ORFs
subsetSamples | Filter results by sample
subsetTax | Filter results by taxonomy
summary.SQM | summary method for class SQM
summary.SQMbunch | summary method for class SQMbunch
summary.SQMlite | summary method for class SQMlite
USiCGs | Universal Single-Copy Genes