Function reference • archR

Main functions Most basic functions
`archR()`	archR: A package for de novo discovery of different sequence architectures
`archR_set_config()`	Set archR run configuration
Prepare input Functions enabling preparation of input
`prepare_data_from_FASTA()`	Generate one-hot encoding of sequences given as FASTA file
`get_one_hot_encoded_seqs()`	Get one-hot encoded sequences
Getter functions Getter functions for archR result object
`get_clBasVec()` `get_clBasVec_k()` `get_clBasVec_m()` `get_seqClLab()`	Get functions for archR result object
`seqs_str()`	Get sequences from the archR result object
Visualization functions Functions enabling visualization of intermediate and final output
`plot_arch_for_clusters()`	Plot cluster architectures as sequence logos.
`plot_ggseqlogo_of_seqs()`	Plot sequence logo of a collection of sequences
`viz_bas_vec_heatmap_seqlogo()` `viz_bas_vec_seqlogo()` `viz_bas_vec_heatmap()`	Visualize the NMF basis vectors in a paired heatmap and sequence logo plot
`plot_ggheatmap()`	Plot a given position weight matrix as a heatmap using ggplot2
`plot_ggseqlogo()`	Visualize a given (PWM) matrix as a sequence logo.
`viz_seqs_acgt_mat_from_seqs()`	Visualize raw DNA sequences as an image
Manipulate archR result Functions to manipulate elements from archR result
`collate_archR_result()`	Collate raw clusters at the chosen iteration of archR result
`get_seqs_clust_list()`	Retrieve sequence clusters as a list from the sequence labels
`make_sinuc_PWMs()`	Make a PWM-resembling matrix out of a given n-vector
`make_dinuc_PWMs()`	Similarly to the PWM-like matrix for mononucleotides, make one for dinucleotides
Shiny app Use archR via its shiny app
`run_archR_UI()`	Launch archR's graphical user interface

Reference

Main functions

Prepare input

Getter functions

Visualization functions

Manipulate archR result

Shiny app