Man pages for johnmcculloch/JAMS_BW
Just A Microbiology System

add_blast_results_to_featuredataadd_interpro_to_featuredata
add_interpro_to_featuredataadd_interpro_to_featuredata
adjust_phenotableadjust_phenotable(opt = NULL, list.data = NULL,...
agglomerate_featuresagglomerate_features(ExpObj = NULL, glomby = NULL)
annotate_contigsannotate_contigs
assemble_contigsassemble_contigs
bank_readsbank_reads
blast_databasesblast_databases
calculate_matrix_statscalculate_matrix_stats(countmatrix=NULL, uselog=NULL,...
can_be_made_numericcan_be_made_numeric(x, cats_to_ignore = NULL) Returns logical...
check_resourcescheck_resources(opt=opt)
classify_16S_from_contigsclassify_16S_from_contigs(opt=opt)
compare_samplescompare_samples(mgseqobj=NULL, mgSeqnorm=FALSE, glomby=NULL,...
compare_ucobiascompare_ucobias
compose_metadatacompose_metadata
compute_readcountscompute_readcounts(opt=opt)
compute_signature_numbasescompute_signature_numbases
consolidate_tablesconsolidate_tables(opt=opt)
convert_matrix_log2convert_matrix_log2(mat = NULL, transformation = NULL)
countfastqcountfastq(fastqfile) Wrapper for counting number of reads...
countfastq_filescountfastq_files(fastqfiles = NULL, threads = NULL) Wrapper...
declare_filtering_presetsdeclare_filtering_presets(analysis = NULL, applyfilters =...
deconvolute_contaminated_isolatesdeconvolute_contaminated_isolates This function is...
define_kinds_of_variablesdefine_kinds_of_variables(metadataXL = NULL, phenolabels =...
detectHardwareResourcesdetectHardwareResources() Generic function for getting number...
evaluate_assemblyevaluate_assembly(opt=NULL)
ExpObjVettingExpObjVetting(ExpObj = NULL)
export_expvec_to_XLexport_expvec_to_XL(expvec = NULL, usefulexp = NULL, filename...
export_from_listexport_from_list
exporttabletsvexporttabletsv(dataobj = NULL, project = NULL, basename =...
filetypefiletype(path) Wrapper for returning class of system file.
filter_correlationsfilter_correlations(corrmat = NULL, mincorrelcoeff = NULL)...
filter_experimentfilter_experiment(ExpObj = NULL, featmaxatleastPPM = 0,...
filter_hostfilter_host
filter_sample_by_class_to_ignorefilter_sample_by_class_to_ignore(SEobj = NULL, mgseqobj =...
filter_sequence_by_lengthfilter_sequence_by_length(sequence=NULL, minlength=0,...
filter_sequence_by_namefilter_sequence_by_name(input_sequences=NULL,...
find_accession_from_keytermfind_accession_from_keyterm(ExpObj = NULL, keyterm = NULL)
fix_interproscanoutputfix_interproscanoutput
fix_krakenfix_kraken(taxtable)
fix_qiime2_taxonomyConvert qiime2 taxonomy table to one compatible with JAMS
gather_run_infogather_run_info
get_contig_coverageget_contig_coverage
get_contigsget_contigs
get_feature_statsget_feature_stats
get_feature_to_accession_tableget_feature_to_accession_table
get_feature_to_accession_table_parallelget_feature_to_accession_table_parallel
get_feature_to_blast_result_tableget_feature_to_blast_result_table
get_genome_completenessget_genome_completeness<-function(pheno=pheno,...
get_genomes_NCBIget_genomes_NCBI(organisms="bacteria", assembly_summary=NULL,...
getOrdinalNumber1Author: Phillip Burger Date: Sept 3, 2014 Purpose: Get the...
get_readsget_reads
get_sequence_statsget_sequence_stats
harvest_functionsharvest_functions
infer_LKTinfer_LKT
IO_jams_workspace_imageIO_jams_workspace_image(opt = NULL, workspaceimage = NULL,...
kraken_classify_taxonomykraken_classify_taxonomy
launch_interprolaunch_interpro
load_jamsfiles_from_systemload_jamsfiles_from_system(path = ".", recursive = TRUE,...
load_metadata_from_fileload_metadata_from_file(xlsxFile = NULL, phenotable_tsv =...
load_qiime2_dataload qiime2 files into metagenomeSeq object
log2PPMtoPctlog2PPMtoPct(log2PPM)
make_alpha_reportmake_alpha_report(project=NULL, expvec=NULL, usefulexp=NULL,...
make_antibiogram_experimentmake_antibiogram_experiment(mgseqresfinder = NULL,...
make_colour_dictionarymake_colour_dictionary(variable_list=NULL, pheno=NULL)
make_heatmap_reportmake_heatmap_report(report = "comparative", project = NULL,...
make_jams_filemake_jams_file
make_metadata_from_taxtablemake_metadata_from_taxtable(taxlvlinterest = NULL,...
make_metagenomeSeq_experimentsmake_metagenomeSeq_experiments(pheno = NULL, onlysamples =...
make_ordination_reportmake_ordination_report(project = NULL, algorithm = "PCA",...
make_readdatamake_readdata(Samples=NULL, list.data=NULL)
make_sequences_capsmake_sequences_caps(sequence=NULL)
make_SummarizedExperimentsmake_SummarizedExperiments(pheno = NULL, onlysamples = NULL,...
name_samplesname_samples(list.data=NULL)
pareto_abundancepareto_abundance(LKTdose=NULL, samplename=NULL,...
Pct2log2PPMPct2log2PPM(Pct)
plot_alpha_diversityplot_alpha_diversity(mgseqobj=NULL, glomby=NULL,...
plot_bar_graphCreates bar graph of relative taxonomic abundance from...
plot_biasplot_bias(bias, method = c("pca", tSNE"), frac = 0.25))
plot_correlation_heatmapplot_correlation_heatmap(ExpObj = NULL, glomby = NULL,...
plot_duet_heatmapplot_duet_heatmap(mgseqobj = NULL, glomby = NULL,...
plot_feature_relabundplot_feature_relabund<-function(ExpObj=NULL, mgSeqnorm=FALSE,...
plot_Ordinationplot_Ordination(ExpObj = NULL, glomby = NULL, subsetby =...
plot_readdataplot_readdata(readdata=NULL)
plot_readscatterplot_readscatter(opt = NULL)
plot_relabund_heatmapplot_relabund_heatmap(ExpObj = NULL, glomby = NULL, hmtype =...
plot_relabund_heatmap_mgseqplot_relabund_heatmap_mgseq(mgseqobj = NULL, glomby = NULL,...
plot_VennCreates Venn Diagram (2, 3, or 4 way) from metagenomeSeq...
plot_wordcloud_sampleplot_wordcloud_sample(opt=opt, elements=NULL)
prepare_contigs_for_JAMSprepare_contigs_for_JAMS
print_jams_reportprint_jams_report(opt=opt)
print_tableprint_table(tb=NULL, tabletitle=NULL, fontsize=6, numrows=20)
quietquiet(function(x)) Suppresses output messages By Hadley...
RAMbytes_statusRAMbytes_status(RAMbytesavail = NULL) Reports how much RAM...
randomize_experimentrandomize_experiment(mgseqobj = NULL, newname = "Noise",...
rename_sequences_consecutivelyrename_sequences_consecutively(sequence=NULL, sequence=NULL,...
sample_by_categorysample_by_category
shrink_perbasecoverageshrink_perbasecoverage(perbasecoverage=NULL, percentage=2)
spew_heatmap_reportspew_heatmap_report(c("analysis", "report")) Wrapper for...
SraRunTable_to_metadataSraRunTable_to_metadata(SraRunTable=NULL, Sample=NULL,...
trim_readstrim_reads
trim_whitespace_from_dftrim_whitespace_from_df(df) Trims leading and trailing...
whoopsieplotwhoopsieplot(msg = NULL) Shuts down the device and gives a...
johnmcculloch/JAMS_BW documentation built on Feb. 11, 2020, 9:22 p.m.