Function reference • seqArchR

Main functions Most basic functions
`seqArchR()`	seqArchR: A package for de novo discovery of different sequence architectures
`set_config()`	Set seqArchR 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 seqArchR result object
`get_clBasVec()` `get_clBasVec_k()` `get_clBasVec_m()` `get_seqClLab()`	Get functions for seqArchR result object
`seqs_str()`	Get sequences from the seqArchR 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_pwm()`	Visualize a position weight matrix as a heatmap or sequence logo
`viz_bas_vec()`	Visualize the NMF basis vectors
`viz_seqs_acgt_mat()`	Visualize raw DNA sequences as an image
Manipulate seqArchR result Functions to manipulate elements from seqArchR result
`collate_seqArchR_result()`	Collate raw clusters at the chosen iteration of seqArchR result
`collate_clusters()`	Collate sequence IDs from an existing clustering according to a new, given clustering of the existing clusters
`get_seqs_clust_list()`	Retrieve sequence clusters as a list from the sequence labels
`make_PWMs()`	Make a PWM-resembling matrix out of a given n-vector

Reference