Package index • strollur

Getting Started

Adding and using data

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
names(): Get the names of various data in a strollur object
count(): Find the number of sequences, samples, treatments or bins of a given type in a strollur object
abundance(): Get the abundance data for sequences, bins, samples, and treatments in a strollur object
report(): Get a data.frame containing the given report in a strollur object
summary(): Summarize the sequences data, custom reports, and scrapped data in a strollur object
strollur: The strollur::strollur object
strollur-package: strollur: Store and Transfer Amplicon Sequence Data

Importing Data

Importing from other software tools namely: mothur, qiime2, phyloseq and DADA2

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
unpack_qiime2_artifact(): The unpack_qiime2_artifact function reads .qza files created by qiime2, and returns the artifact.

General

Create datasets and references, clear data

miseq_sop_example(): Create a strollur object using the analysis files from the MiSeq_SOP example.
new_dataset(): Create a new strollur object
new_reference(): Create a resource reference for your strollur object to aid in reproducibility.
clear(): Clear data from a strollur object
is_aligned(): Determine if a strollur object contains aligned sequences.
is_equal(): is_equal
has_sample(): Determine if a given sample is in a strollur object
get_bin_types(): Get bin table types of a strollur object

Data Transfers

Save, copy, load, import, export and write to file

save_dataset(): Save the strollur object to file.
load_dataset(): Load a strollur object from a file.
export_dataset(): Create a human readable table containing all data from a strollur object.
import_dataset(): Create a strollur object from the exported table of a strollur object object.
copy_dataset(): Create a new strollur object from an existing dataset.
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

Functions for Package Developers

Want to create and modify strollur objects from your package? Check out these functions

strollur_example(): strollur_example
has_sequence_strings(): Determine if a strollur object contains sequence nucleotide strings.
remove_file(): remove_file
sort_dataframe(): sort_dataframe
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_sequence_fastq_scores(): Add FASTQ data to a strollur object
xdev_add_sequences(): Add sequence data 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_bins(): Add bin assignments 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_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_get_sequences(): Get the nucleotide strings for each sequence in a strollur object
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