Store and Transfer Amplicon Sequence Data

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Documentation for package ‘strollur’ version 0.1.4

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abundance Get the abundance data for sequences, bins, samples, and treatments in a strollur object
add Add sequences, reports, trees or resource references to a strollur object
assign Assign sequence abundances, sequence classifications, bins, bin representative sequences, bin classifications, sample distances or treatments to a strollur object
clear Clear data from a strollur object
copy_dataset Create a new strollur object from an existing dataset.
count Find the number of sequences, samples, treatments or bins of a given type in a strollur object
export_dataset Create a human readable table containing all data from a strollur object.
get_bin_types Get bin table types of a strollur object
has_sample Determine if a given sample is in a strollur object
has_sequence_strings Determine if a strollur object contains sequence nucleotide strings.
import_dataset Create a strollur object from the exported table of a strollur object
is_aligned Determine if a strollur object contains aligned sequences.
is_equal Determine if two strollur objects are equal.
load_dataset Load a strollur object from a file.
miseq_sop_example Create a strollur object using the analysis files from the MiSeq_SOP example.
names Get the names of various data in a strollur object
new_dataset Create a new strollur object
new_reference Create a resource reference for your strollur object to aid in reproducibility.
read_biom Create a strollur object from a biom formatted file.
read_dada2 Create a strollur object from dada2 outputs
read_fasta Read a FASTA formatted sequence file
read_fastq Read a FASTQ formatted file
read_mothur Create a strollur object from mothur outputs
read_mothur_cons_taxonomy Read a mothur formatted cons_taxonomy file
read_mothur_count Read a mothur formatted count file
read_mothur_list Read a mothur formatted list file
read_mothur_oligos Read a mothur formatted oligos file
read_mothur_rabund Read a mothur formatted rabund file
read_mothur_shared Read a mothur formatted shared file
read_mothur_taxonomy Read a mothur formatted taxonomy file
read_phyloseq Create a strollur object from a phyloseq object
read_qiime2 Create a strollur object from a qiime2 outputs
read_qiime2_feature_table Read a qiime2 qza containing bin data
read_qiime2_metadata Read a qiime2 .tsv table containing metadata.
read_qiime2_taxonomy Read a qiime2 qza containing taxonomy data
read_quality Read a file containing sequence quality scores
remove_file remove_file
report Get a data.frame containing the given report in a strollur object
save_dataset Save the strollur object to file.
sort_dataframe sort_dataframe
strollur The 'strollur::strollur' object
strollur_example strollur_example
summary Summarize the sequences data, custom reports, and scrapped data in a strollur object
unpack_qiime2_artifact The unpack_qiime2_artifact function reads .qza files created by qiime2, and returns the artifact.
write_biom Write a BIOM formatted file containing a strollur object's data.
write_fasta Write a FASTA formatted sequence file
write_fastq Write a FASTQ formatted file
write_mothur Write the various file types from your strollur object for use with mothur.
write_mothur_cons_taxonomy Write a mothur formatted cons_taxonomy file
write_mothur_count Write a mothur formatted count file
write_mothur_design Write a mothur formatted design file
write_mothur_list Write mothur formatted list files
write_mothur_rabund Write mothur formatted rabund files
write_mothur_shared Write mothur formatted shared files
write_phyloseq Create a phyloseq object from your strollur object
write_quality Write a file containing sequence quality scores
write_taxonomy Write a 2 column taxonomy file
xdev_abundance Get a data.frame containing the requested abundance data
xdev_add_references Add resource references to a strollur object to aid in reproducibility
xdev_add_report Add a report to a strollur object
xdev_add_sequences Add sequence data to a strollur object
xdev_add_sequence_fastq_scores Add FASTQ data to a strollur object
xdev_assign_bins Add bin assignments to a strollur object
xdev_assign_bin_representative_sequences Assign representative sequences to bins
xdev_assign_bin_taxonomy Assign bin classifications to a strollur object
xdev_assign_bin_taxonomy_tidy Assign bin classifications to a strollur object
xdev_assign_sample_distances Assign samples distances in a strollur object
xdev_assign_sequence_abundance Assign sequence abundance and optionally assign sample and treatment data to a strollur object
xdev_assign_sequence_quality_scores Add quality data to a strollur object
xdev_assign_sequence_taxonomy Assign sequence classifications to a strollur object
xdev_assign_sequence_taxonomy_tidy Assign sequence classifications to a strollur object
xdev_assign_treatments Assign samples to treatments in a strollur object
xdev_count Find the number of sequences, samples, treatments or bins of a given type in a strollur object
xdev_get_abundances_by_sample Get the sequence abundance data in a strollur object parsed by sample
xdev_get_alignment_length Get the alignment length of sequences in your strollur object
xdev_get_bin_abundances_by_sample Get the sequence abundance data in a strollur object parsed by sample
xdev_get_by_sample Get the requested data in a strollur object parsed by sample
xdev_get_list_vector Get vector of strings containing the sequences bin data
xdev_get_sample_distances Get distances between samples in your 'strollur object
xdev_get_sequences Get the nucleotide strings for each sequence in a strollur object
xdev_get_sequence_abundances_by_sample Get the sequence abundance data in a strollur object parsed by sample
xdev_get_sequence_indexes_by_sample Get indexes of sequences parsed by sample
xdev_has_bin_taxonomy Determine if a strollur object has bin taxonomy assignments
xdev_has_sequence_taxonomy Determine if a strollur object has sequence taxonomy assignments
xdev_merge_bins Merge bins in your strollur object
xdev_merge_sequences Merge sequences combines the abundances of sequences
xdev_names Get the names of a given type of data in a strollur object
xdev_remove_bins Remove bins from a strollur object
xdev_remove_lineages Remove contaminants from a strollur object
xdev_remove_samples Remove samples from a strollur object
xdev_remove_sequences Remove sequences from a strollur object
xdev_report Get a data.frame containing the given report in a strollur object
xdev_set_abundance Set abundances of sequences in a strollur object without sample data
xdev_set_abundances Set abundances of sequences in a strollur object with sample data
xdev_set_dataset_name Set the name of a strollur object
xdev_set_sequences Set neucleotide sequence string in a strollur object