Man pages for johnmcculloch/JAMS_BW
Just A Microbiology System

add_blast_results_to_featuredataadd_blast_results_to_featuredata
add_interpro_to_featuredataadd_interpro_to_featuredata
add_shape_to_plot_safelyadd_shape_to_plot_safely(p = NULL, shapevec = NULL, shapeby =...
adjust_phenotableadjust_phenotable(opt = NULL, list.data = NULL,...
agglomerate_featuresagglomerate_features(ExpObj = NULL, glomby = NULL)
analyze_fastq_filenameanalyze_fastq_filename(fn = NULL, maintain_Illumina_format =...
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, application = "WGS")
classify_16S_from_contigsclassify_16S_from_contigs(opt=opt)
compare_ucobiascompare_ucobias
compute_readcountscompute_readcounts(opt=opt)
compute_signature_numbasescompute_signature_numbases
compute_x_fontcompute_x_font(nx = 1, upper_n = 400, upper_fs = 0.1, lower_n...
consolidate_tablesconsolidate_tables(opt=opt)
constrain_JAMS_SEobj_to_wanted_taxaConstrains a functional (non-taxonomic) JAMS-style...
convert_matrix_log2convert_matrix_log2(mat = NULL, transformation = NULL)
convert_matrix_PAconvert_matrix_PA(mat = NULL, threshPA = 0)
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)
evaluate_metaBAT_binevaluate_metaBAT_bin(opt=NULL)
evaluate_metaBAT_bin_CheckMevaluate_metaBAT_bin_CheckM(opt=NULL)
ExpObjVettingExpObjVetting(ExpObj = NULL)
export_expvec_to_XLExports counts and featuredata in a SummarizedExperiment...
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, variables =...
filter_sequence_by_lengthfilter_sequence_by_length(sequence=NULL, minlength=0,...
filter_sequence_by_namefilter_sequence_by_name(input_sequences = NULL, sequencenames...
find_accession_from_keytermfind_accession_from_keyterm(ExpObj = NULL, keyterm = NULL)
find_clusters_in_matrixfind_clusters_in_matrix(input_matrix = NULL, kmeans_split =...
fix_interproscanoutputfix_interproscanoutput(opt = NULL, check_ipro_jobs_status =...
fixrelpathfixrelpath(JAMSpath = NULL)
gather_run_infogather_run_info
generate_filenamegenerate_filename(title = "ABC_look_at_me", add_date = TRUE,...
get_contig_coverageget_contig_coverage(opt = NULL, markduplicates = FALSE,...
get_contigsget_contigs
get_feature_statsget_feature_stats
get_feature_to_accession_tableget_feature_to_accession_table
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
hm_fontsize_computerhm_fontsize_computer(mat_rownames = NULL, mat_colnames =...
infer_column_typeinfer_column_type(phenotable = NULL, colm = NULL,...
infer_LKTinfer_LKT
infer_LKT_pr2infer_LKT_pr2
install_biocon_depsinstall_biocon_deps()
IO_jams_workspace_imageIO_jams_workspace_image(opt = NULL, workspaceimage = NULL,...
is.redundantis.redundant(vec)
is.usefulis.useful(vec)
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 =...
log2PPMtoPctlog2PPMtoPct(log2PPM)
make_antibiogram_experimentmake_antibiogram_experiment(mgseqresfinder = NULL,...
make_colour_dictionarymake_colour_dictionary(variable_list = NULL, pheno = NULL,...
make_featuredata_from_bedfilemake_featuredata_from_bedfile
make_jams_filemake_jams_file
make_metadata_from_taxtablemake_metadata_from_taxtable(taxlvlinterest = NULL,...
make_phenolabels_from_phenotablemake_phenolabels_from_phenotable(phenotable = NULL)
make_readdatamake_readdata(Samples=NULL, list.data=NULL)
make_sequences_capsmake_sequences_caps(sequence = NULL)
make_SummarizedExperiment_from_tablesmake_SummarizedExperiment_from_tables(pheno = NULL, pheno_fn=...
make_SummarizedExperimentsmake_SummarizedExperiments(pheno = NULL, onlysamples = NULL,...
merge_JAMS_SEobjSafely merges two compatible JAMS-style SummarizedExperiment...
merge_sparse_matrixSafely merges two sparse matrices. This function was written...
name_samplesname_samples(list.data = NULL)
pareto_abundancepareto_abundance(LKTdose=NULL, samplename=NULL,...
Pct2log2PPMPct2log2PPM(Pct)
plot_alpha_diversityGenerates relative abundance plots per feature annotated by...
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_genome_taxonomy_donutplot_genome_taxonomy_donut(opt = opt, contigsdata = NULL)
plot_OrdinationCreates ordination plots based on PCA, tSNE or tUMAP
plot_readdataplot_readdata(readdata=NULL)
plot_readscatterplot_readscatter(opt = NULL)
plot_relabund_featuresplot_relabund_features(ExpObj = NULL, glomby = NULL,...
plot_relabund_heatmapPlots relative abundance heatmaps annotated by the metadata...
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...
rename_sequences_consecutivelyrename_sequences_consecutively(sequence=NULL, sequence=NULL,...
replace_NAs_with_characterreplace_NAs_with_character(df) Replaces NAs with a specific...
replace_Sample_names_in_SEobjreplace_Sample_names_in_SEobj(curr_SEobj = NULL,...
retrieve_features_by_taxaretrieve_features_by_taxa(FuncExpObj = NULL, assay_for_matrix...
sample_by_categorysample_by_category
shrink_perbasecoverageshrink_perbasecoverage(perbasecoverage=NULL, percentage=2)
spew_heatmap_reportspew_heatmap_report(c("analysis", "report")) Wrapper for...
split_featnamesplit_featname(featname = NULL, thresh_featname_split = 40)
SraRunTable_to_metadataSraRunTable_to_metadata(SraRunTable=NULL, Sample=NULL,...
trim_readstrim_reads
trim_whitespace_from_dftrim_whitespace_from_df(df) Trims leading and trailing...
update_ExpObj_metadataupdate_ExpObj_metadata(ExpObj = NULL, phenotable = NULL)
whoopsieplotwhoopsieplot(msg = NULL) Shuts down the device and gives a...
johnmcculloch/JAMS_BW documentation built on Sept. 1, 2024, 12:48 a.m.