Package index • strollur

Getting Started

Adding and using data

add(): Add sequences, reports, metadata or resource references to a strollur object
assign(): Assign sequence abundances, sequence classifications, bins, bin representative sequences, bin classifications 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` object stores the data associated with your microbial analysis.
strollur-package: strollur: Store and Transfer Data Used in the Analysis of Microbial RNA

Importing Data

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

read_dada2(): Create a strollur object from dada2 outputs
read_fasta(): read_fasta
read_mothur(): Create a strollur object from mothur outputs
read_mothur_cons_taxonomy(): read_mothur_cons_taxonomy
read_mothur_count(): read_mothur_count
read_mothur_list(): read_mothur_list
read_mothur_rabund(): read_mothur_rabund
read_mothur_shared(): read_mothur_shared
read_mothur_taxonomy(): read_mothur_taxonomy
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_qiime2_feature_table
read_qiime2_metadata(): read_qiime2_metadata
read_qiime2_taxonomy(): read_qiime2_taxonomy
unpack_qiime2_artifact(): unpack_qiime2_artifact

General

Create datasets and references, clear data

miseq_sop_example(): Example strollur object
new_dataset(): new_dataset
new_reference(): new_reference
clear(): clear
is_aligned(): is_aligned
has_sample(): has_sample
get_bin_types(): get_bin_types

Data Transfers

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

save_dataset(): save_dataset
load_dataset(): Load strollur object from .rds file
export_dataset(): export_dataset
import_dataset(): Import strollur object from exported data.frame.
copy_dataset(): copy_dataset
write_fasta(): write_fasta
write_mothur(): write_mothur
write_mothur_cons_taxonomy(): write_mothur_cons_taxonomy
write_mothur_count(): write_mothur_count
write_mothur_design(): write_mothur_design
write_mothur_list(): write_mothur_list
write_mothur_rabund(): write_mothur_rabund
write_mothur_shared(): write_mothur_shared
write_phyloseq(): write_phyloseq
write_taxonomy(): write_taxonomy

Functions for Package Developers

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

strollur_example(): strollur_example
get_available_processors(): Get available processors
has_sequence_strings(): has_sequence_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
xdev_add_report(): Add a report to a strollur object
xdev_add_sequences(): xdev_add_sequences
xdev_assign_bin_representative_sequences(): xdev_assign_bin_representative_sequences
xdev_assign_bin_taxonomy(): xdev_assign_bin_taxonomy
xdev_assign_bins(): xdev_assign_bins
xdev_assign_sequence_abundance(): xdev_assign_sequence_abundance
xdev_assign_sequence_taxonomy(): xdev_assign_sequence_taxonomy
xdev_assign_sequence_taxonomy_tidy(): xdev_assign_sequence_taxonomy_tidy
xdev_assign_treatments(): xdev_assign_treatments
xdev_count(): xdev_count
xdev_get_abundances_by_sample(): xdev_get_abundances_by_sample
xdev_get_by_sample(): xdev_get_by_sample
xdev_get_list_vector(): xdev_get_list_vector
xdev_get_sequences(): xdev_get_sequences
xdev_has_sequence_taxonomy(): xdev_has_sequence_taxonomy
xdev_merge_bins(): xdev_merge_bins
xdev_merge_sequences(): xdev_merge_sequences
xdev_names(): xdev_names
xdev_remove_bins(): xdev_remove_bins
xdev_remove_lineages(): xdev_remove_lineages
xdev_remove_samples(): xdev_remove_samples
xdev_remove_sequences(): xdev_remove_sequences
xdev_report(): xdev_report
xdev_set_abundance(): xdev_set_abundance
xdev_set_abundances(): xdev_set_abundances
xdev_set_dataset_name(): xdev_set_dataset_name
xdev_set_num_processors(): xdev_set_num_processors
xdev_set_sequences(): xdev_set_sequences
xdev_summarize(): xdev_summarize