archR: archR: A package for de novo discovery of different sequence...
In snikumbh/archR: Identify Different Architectures of Sequence Elements

Description Usage Arguments Details Value Functions for data preparation and manipulation Functions for visualizations Examples

View source: R/archR_main.R

Given a set of DNA sequences, archR enables unsupervised discovery of _de novo_ clusters with characteristic sequence architectures characterized by position-specific motifs or composition of stretches of nucleotides, e.g., CG-richness, etc.

Call this function to process a data set using archR.

archR(
  config,
  seqs_ohe_mat,
  seqs_raw,
  seqs_pos = NULL,
  total_itr = NULL,
  set_ocollation = NULL,
  fresh = TRUE,
  use_oc = NULL,
  o_dir = NULL
)

`config`	archR configuration object as returned by `archR_set_config`. This is a required argument.
`seqs_ohe_mat`	A matrix of one-hot encoded sequences with sequences along columns. This is a required argument.
`seqs_raw`	A `DNAStringSet` object. The FASTA sequences as a DNAStringSet object. This argument required argument.
`seqs_pos`	Vector. Specify the tick labels for sequence positions. Default is NULL.
`total_itr`	Numeric. Specify the number of iterations to perform. This should be greater than zero. Default is NULL.
`set_ocollation`	Logical vector. A logical vector of length 'total_itr' specifying for every iteration of archR if collation of clusters from outer chunks should be performed. TRUE denotes clusters are collated, FALSE otherwise.
`fresh`	Logical. Specify if this is (not) a fresh run. Because archR enables checkpointing, it is possible to perform additional iterations upon clusters from an existing archR result (or a checkpoint) object. See 'use_oc' argument. For example, when processing a set of FASTA sequences, if an earlier call to archR performed two iterations, and now you wish to perform a third, the arguments 'fresh' and 'use_oc' can be used. Simply set 'fresh' to FALSE and assign the sequence clusters from iteration two from the earlier result to 'use_oc'. As of v0.1.3, with this setting, archR returns a new result object as if the additional iteration performed is the only iteration.
`use_oc`	List. Clusters to be further processed with archR. These can be from a previous archR result (in which case use `get_seqs_clust_list` function), or simply clusters from any other method. Warning: This has not been rigorously tested yet (v0.1.3).
`o_dir`	Character. Specify the output directory with its path. archR will create this directory. If a directory with the given name exists at the given location, archR will add a suffix to the directory name. This change is reported to the user. Default is NULL. When NULL, just the result is returned, and no plots or checkpoints or result is written to disk.

The archR package provides three categories of important functions: related to data preparation and manipulation, performing non-negative matrix factorization, performing clustering, and visualization-related functions.

A nested list of elements as follows:

seqsClustLabels: A list with cluster labels for all sequences per iteration of archR. The cluster labels as stored as characters.
clustBasisVectors: A list with information on NMF basis vectors per iteration of archR. Per iteration, there are two variables 'nBasisVectors' storing the number of basis vectors after model selection, and 'basisVectors', a matrix storing the basis vectors themselves. Dimensions of the 'basisVectors' matrix are 4*L x nBasisVectors (mononucleotide case) or 16*L x nBasisVectors (dinucleotide case).
clustSol: The clustering solution obtained upon processing the raw clusters from the last iteration of archR's result. This is handled internally by the function collate_archR_result using the default setting of Euclidean distance and ward.D linkage hierarchical clustering.
rawSeqs: The input sequences as a DNAStringSet object.
timeInfo: Stores the time taken (in minutes) for processing each iteration. This element is added only if 'time' flag is set to TRUE in config.
config: The configuration used for processing.
call: The function call itself.

prepare_data_from_FASTA
get_one_hot_encoded_seqs

plot_arch_for_clusters
plot_ggseqlogo_of_seqs
viz_bas_vec_heatmap
viz_bas_vec_seqlogo
viz_bas_vec_heatmap_seqlogo
viz_seqs_acgt_mat_from_seqs
plot_ggseqlogo
plot_ggheatmap

fname <- system.file("extdata", "example_data.fa",
                        package = "archR", mustWork = TRUE)

# Specifying 'dinuc' generates dinucleotide features
inputSeqsMat <- archR::prepare_data_from_FASTA(fasta_fname = fname,
    sinuc_or_dinuc = "dinuc")

inputSeqsRaw <- archR::prepare_data_from_FASTA(fasta_fname = fname,
    raw_seq = TRUE)

# Set archR configuration
archRconfig <- archR::archR_set_config(
    parallelize = TRUE,
    n_cores = 2,
    n_runs = 100,
    k_min = 1,
    k_max = 20,
    mod_sel_type = "stability",
    bound = 10^-8,
    chunk_size = 100,
    flags = list(debug = FALSE, time = TRUE, verbose = TRUE,
        plot = FALSE)
)

# Run archR
archRresult <- archR::archR(config = archRconfig,
                          seqs_ohe_mat = inputSeqsMat,
                          seqs_raw = inputSeqsRaw,
                          seqs_pos = seq(1,100,by=1),
                          total_itr = 2,
                          set_ocollation = c(TRUE, FALSE))